Contacts of the helix formed by residues 2661 - 2682 (chain A) in PDB entry 4ERV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR2661 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2655A ARG* 4.6 5.6 - - - +
2659A THR 3.8 1.0 + - - +
2660A LEU* 1.3 74.7 - - - +
2662A GLU* 1.3 66.3 + - - +
2663A LYS* 3.6 9.0 + - - +
2664A GLU* 2.9 45.1 + - - +
2665A LYS* 2.9 22.2 + - - +
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Residues in contact with GLU2662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2660A LEU 3.9 0.6 + - - -
2661A THR* 1.3 73.2 - - - +
2663A LYS* 1.3 59.6 + - + +
2665A LYS* 3.3 12.0 + - - +
2666A GLU* 2.9 31.8 + - + +
2669A ARG* 2.7 41.5 + - - -
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Residues in contact with LYS2663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2661A THR* 3.2 7.7 + - - +
2662A GLU* 1.3 80.0 - - + +
2664A GLU* 1.3 62.4 + - + +
2666A GLU* 3.1 8.3 + - + +
2667A ILE* 3.1 31.4 + - + +
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Residues in contact with GLU2664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2653A LEU* 3.9 23.1 - - + +
2655A ARG* 2.9 29.8 + - - -
2660A LEU* 3.7 15.3 - - + +
2661A THR* 2.9 35.4 + - - +
2663A LYS* 1.3 76.7 - - + +
2665A LYS* 1.3 62.7 + - - +
2666A GLU 3.5 0.2 + - - -
2667A ILE* 3.5 20.7 + - + +
2668A TYR* 3.4 20.0 - - + -
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Residues in contact with LYS2665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2657A PHE* 3.4 59.7 - - + +
2658A LYS* 4.1 16.7 + - - +
2660A LEU* 3.7 17.5 - - + -
2661A THR 2.9 14.9 + - - +
2662A GLU* 3.5 16.3 + - - +
2664A GLU* 1.3 76.7 - - - +
2666A GLU* 1.3 62.5 + - - +
2668A TYR* 3.1 9.0 + - - +
2669A ARG* 3.1 47.1 + - - +
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Residues in contact with GLU2666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2662A GLU* 2.9 20.6 + - + +
2663A LYS* 3.1 9.6 + - - +
2665A LYS* 1.3 74.2 - - - +
2667A ILE* 1.3 60.2 + - + +
2669A ARG* 3.0 22.6 + - - +
2670A TRP* 2.9 44.4 + - + +
2673A ARG* 2.8 44.8 + - - -
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Residues in contact with ILE2667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2663A LYS* 3.1 18.3 + - + +
2664A GLU* 3.7 20.6 - - + +
2665A LYS 3.2 0.4 - - - -
2666A GLU* 1.3 76.7 - - - +
2668A TYR* 1.3 65.5 + - + +
2670A TRP* 4.4 2.9 - - - +
2671A PRO* 3.4 19.1 - - - +
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Residues in contact with TYR2668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2621A TYR* 5.6 0.7 - - - -
2622A ALA* 3.7 26.7 - - + +
2625A SER* 4.0 18.5 + - - -
2626A HIS* 2.8 64.2 + + + -
2629A TRP* 3.9 23.0 - + + -
2653A LEU* 4.8 11.1 - - + +
2657A PHE* 4.2 8.3 - + - -
2660A LEU* 3.9 10.1 - - + -
2664A GLU* 3.4 20.6 - - + -
2665A LYS 3.1 6.6 + - - +
2667A ILE* 1.3 83.5 - - + +
2669A ARG* 1.3 64.2 + - - +
2671A PRO* 3.6 12.7 - - - +
2672A ALA* 4.4 6.1 + - - +
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Residues in contact with ARG2669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2615A GLU* 5.5 0.7 - - - -
2618A VAL* 3.5 21.2 - - + +
2619A THR* 3.0 33.7 + - - +
2622A ALA* 3.7 17.5 - - + -
2657A PHE* 5.1 1.2 - - + -
2662A GLU* 2.7 42.4 + - - -
2665A LYS* 3.1 35.9 + - - +
2666A GLU* 3.0 39.7 + - - +
2668A TYR* 1.3 77.0 - - - +
2670A TRP* 1.3 65.7 + - - +
2672A ALA* 3.1 5.5 + - - +
2673A ARG* 3.0 32.9 + - - +
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Residues in contact with TRP2670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2666A GLU* 2.9 32.8 + - + +
2667A ILE* 4.4 2.7 - - - +
2669A ARG* 1.3 78.3 - - - +
2671A PRO* 1.3 78.8 - - + +
2673A ARG* 3.4 15.4 + - - +
2674A GLU* 3.1 54.7 + - + +
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Residues in contact with PRO2671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2667A ILE 3.4 19.3 - - - +
2668A TYR* 3.6 10.8 - - - +
2670A TRP* 1.3 106.9 - - + +
2672A ALA* 1.3 57.2 + - - +
2674A GLU* 3.5 2.8 + - + +
2675A SER* 2.9 33.1 + - - -
2783A LYS* 3.9 28.5 + - - +
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Residues in contact with ALA2672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2618A VAL* 4.4 16.4 - - + +
2621A TYR* 3.6 36.1 - - + -
2668A TYR 4.5 4.5 - - - +
2669A ARG 3.1 10.2 + - - +
2671A PRO* 1.3 77.4 - - - +
2673A ARG* 1.3 65.7 + - - +
2675A SER* 3.3 6.9 + - - -
2676A LEU* 3.0 29.3 + - + +
2787A LEU* 4.4 9.4 - - + +
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Residues in contact with ARG2673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2610A LEU* 3.7 19.0 - - + +
2615A GLU* 3.0 30.2 + - - +
2618A VAL* 3.9 14.0 - - + +
2666A GLU* 2.8 42.0 + - - -
2669A ARG* 3.0 30.3 + - - +
2670A TRP* 3.7 22.1 - - - +
2672A ALA* 1.3 76.9 - - - +
2674A GLU* 1.3 61.7 + - - +
2676A LEU* 3.2 4.3 + - - +
2677A LYS* 3.0 54.2 + - - +
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Residues in contact with GLU2674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2605A THR* 3.4 24.8 + - + +
2670A TRP* 3.1 63.5 + - + +
2671A PRO 4.0 3.6 - - - +
2673A ARG* 1.3 82.5 + - - +
2675A SER* 1.3 52.5 + - - +
2677A LYS* 3.2 33.0 + - - +
2678A THR* 2.8 37.9 + - - +
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Residues in contact with SER2675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2671A PRO 2.9 21.6 + - - -
2672A ALA* 3.5 1.8 - - - -
2673A ARG 3.2 0.4 - - - -
2674A GLU* 1.3 76.8 - - - +
2676A LEU* 1.3 61.4 + - - +
2678A THR* 3.2 10.2 + - - -
2679A MET* 3.1 28.8 + - - +
2739A VAL* 5.4 3.9 - - - +
2743A TYR* 2.6 37.0 + - - -
2783A LYS* 4.3 1.9 - - - -
2787A LEU* 3.5 26.8 - - - +
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Residues in contact with LEU2676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2610A LEU* 3.9 17.9 - - + -
2614A LEU* 4.2 22.9 - - + +
2617A ILE* 5.1 2.7 - - + -
2618A VAL* 3.8 27.8 - - + +
2672A ALA* 3.0 15.1 + - + +
2673A ARG 3.2 6.3 + - - +
2675A SER* 1.3 74.8 - - - +
2677A LYS* 1.3 63.7 + - - +
2679A MET* 3.2 23.3 + - + +
2680A LEU* 3.2 24.8 + - - +
2686A VAL* 4.6 12.3 - - + +
2787A LEU* 4.4 9.4 - - + -
2791A LEU* 3.8 37.2 - - + -
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Residues in contact with LYS2677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2605A THR* 3.8 20.0 + - + +
2608A PHE* 3.5 36.9 + - + +
2609A SER* 4.5 6.3 - - - +
2610A LEU* 4.0 19.5 - - + +
2615A GLU* 5.7 0.2 - - - -
2673A ARG* 3.0 35.4 + - - +
2674A GLU* 3.2 38.3 + - - +
2675A SER 3.3 0.2 - - - -
2676A LEU* 1.3 75.6 - - - +
2678A THR* 1.3 57.2 + - - +
2680A LEU* 3.3 8.1 + - - +
2681A ALA* 2.9 29.3 + - - +
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Residues in contact with THR2678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2603A ILE* 3.8 23.9 + - + +
2605A THR* 3.7 16.1 - - - +
2674A GLU* 2.8 19.3 + - - +
2675A SER* 3.3 12.8 - - - -
2677A LYS* 1.3 77.3 - - - +
2679A MET* 1.3 57.3 + - - +
2681A ALA* 3.2 3.4 + - - +
2682A VAL* 2.9 31.0 + - + +
2684A TRP* 6.4 0.2 - - + -
2739A VAL* 5.4 13.7 - - + -
2742A ASN* 3.7 28.6 + - + +
2743A TYR* 6.2 0.8 - - - -
2746A ILE* 5.7 1.6 - - - +
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Residues in contact with MET2679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2675A SER* 3.1 13.5 + - - +
2676A LEU* 3.2 27.1 + - + +
2678A THR* 1.3 76.1 - - - +
2680A LEU* 1.3 60.0 + - - +
2682A VAL* 3.4 4.9 - - - +
2683A GLY 3.4 3.6 + - - -
2684A TRP* 2.9 54.7 + - + +
2686A VAL* 4.0 12.3 - - + -
2739A VAL* 4.7 9.2 - - + -
2787A LEU* 3.9 28.5 - - + -
2788A PHE* 3.7 29.4 - - + -
2791A LEU* 4.3 5.8 - - + -
2798A VAL* 4.0 25.4 - - - -
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Residues in contact with LEU2680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2608A PHE* 3.9 30.4 - - + -
2609A SER 4.4 12.1 - - - +
2610A LEU* 3.8 26.9 - - + -
2611A PRO* 5.2 5.8 - - + -
2614A LEU* 5.2 4.3 - - + -
2676A LEU 3.2 10.2 + - - +
2677A LYS* 3.6 9.2 - - - +
2679A MET* 1.3 76.8 - - - +
2681A ALA* 1.3 58.1 + - - +
2683A GLY* 3.1 20.3 + - - -
2684A TRP 3.9 15.8 - - - +
2685A THR* 5.2 0.7 - - - -
2686A VAL* 4.0 27.6 - - + +
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Residues in contact with ALA2681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2603A ILE* 3.7 14.9 - - + +
2604A ASN 3.7 17.9 - - - +
2605A THR* 4.4 3.1 - - - -
2608A PHE* 3.6 32.4 - - + -
2677A LYS 2.9 16.6 + - - +
2678A THR* 3.2 5.1 + - - +
2680A LEU* 1.3 76.5 - - - +
2682A VAL* 1.3 60.9 + - - +
2683A GLY* 3.1 1.3 + - - -
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Residues in contact with VAL2682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2603A ILE* 3.8 28.9 - - + -
2678A THR* 2.9 15.6 + - + +
2679A MET* 3.4 14.8 - - - +
2681A ALA* 1.3 76.1 - - - +
2683A GLY* 1.3 56.6 + - - +
2684A TRP* 3.6 39.1 + - + +
2738A VAL* 4.7 10.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il