Contacts of the helix formed by residues 2912 - 2933 (chain D) in PDB entry 6X34
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 THR2912 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2910D THR 3.9 0.4 + - - -
2911D LEU* 1.3 79.2 - - - +
2913D ALA* 1.3 65.4 + - - +
2914D LYS* 3.4 8.3 - - - -
2915D GLU* 4.0 11.6 - - - +
2916D LYS* 3.2 23.0 + - - +
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Residues in contact with ALA2913 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2912D THR* 1.3 73.5 - - - +
2914D LYS* 1.3 65.1 + - - +
2916D LYS* 3.5 5.8 + - - +
2917D ALA* 3.4 20.3 + - - +
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Residues in contact with LYS2914 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2912D THR* 3.4 5.1 - - - -
2913D ALA* 1.3 80.8 - - - +
2915D GLU* 1.3 61.5 + - - +
2917D ALA* 3.4 17.8 + - - +
2918D ARG* 4.4 2.3 + - - +
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Residues in contact with GLU2915 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2911D LEU* 4.4 9.6 - - + -
2912D THR* 3.6 20.9 + - - +
2913D ALA 3.4 0.4 - - - -
2914D LYS* 1.3 79.8 - - - +
2916D LYS* 1.3 60.7 + - - +
2917D ALA 3.4 0.5 + - - -
2918D ARG* 3.7 15.5 + - - +
2919D ASP* 4.6 1.9 + - - +
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Residues in contact with LYS2916 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2879D ALA* 5.5 0.3 - - - +
2908D TYR 5.7 2.0 - - - +
2911D LEU* 4.9 7.8 - - + +
2912D THR 3.2 18.1 + - - +
2913D ALA* 4.0 7.0 - - - +
2914D LYS 3.3 0.2 - - - -
2915D GLU* 1.3 74.8 - - - +
2917D ALA* 1.3 59.7 + - - +
2918D ARG 3.2 1.3 + - - -
2919D ASP* 3.4 9.2 + - + +
2920D ARG* 3.0 30.4 + - + +
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Residues in contact with ALA2917 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2913D ALA 3.4 11.8 + - - +
2914D LYS* 3.6 14.4 - - - +
2915D GLU 3.2 1.4 - - - -
2916D LYS* 1.3 78.9 - - - +
2918D ARG* 1.3 62.9 + - - +
2920D ARG* 3.9 5.8 - - - +
2921D GLU* 3.1 25.8 + - - +
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Residues in contact with ARG2918 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2914D LYS 4.4 1.6 + - - +
2915D GLU 3.7 11.7 + - - +
2916D LYS 3.2 0.4 - - - -
2917D ALA* 1.3 80.7 - - - +
2919D ASP* 1.3 59.1 + - - +
2921D GLU* 3.9 7.8 + - - +
2922D LYS* 3.9 11.3 + - - +
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Residues in contact with ASP2919 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2879D ALA* 3.4 41.6 - - + +
2882D TYR* 4.8 9.8 - - + +
2883D HIS* 5.1 8.5 - - + +
2915D GLU 4.6 1.1 + - - +
2916D LYS* 3.4 10.3 + - - +
2917D ALA 3.3 0.2 - - - -
2918D ARG* 1.3 77.6 - - - +
2920D ARG* 1.3 65.5 + - - +
2921D GLU 3.3 0.4 - - - -
2922D LYS* 3.5 6.6 + - - +
2923D ALA 3.4 14.4 + - - -
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Residues in contact with ARG2920 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2875D ALA* 5.7 1.5 - - + +
2879D ALA* 3.9 11.1 - - + +
2916D LYS* 3.0 21.7 + - + +
2917D ALA* 4.3 5.2 - - - +
2919D ASP* 1.3 75.0 - - - +
2921D GLU* 1.3 60.2 + - - +
2923D ALA* 4.0 3.1 - - - +
2924D GLN* 2.9 31.7 + - - +
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Residues in contact with GLU2921 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2917D ALA 3.1 19.1 + - - +
2918D ARG* 4.2 5.8 - - - +
2919D ASP 3.3 0.2 - - - -
2920D ARG* 1.3 78.9 - - - +
2922D LYS* 1.3 56.7 + - - +
2924D GLN* 4.0 5.0 - - - +
2925D GLU* 3.0 29.6 + - - +
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Residues in contact with LYS2922 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2882D TYR* 5.8 6.1 - - + -
2918D ARG 3.9 8.9 + - - +
2919D ASP* 3.5 10.1 + - - +
2920D ARG 3.3 0.2 - - - -
2921D GLU* 1.3 79.4 - - - +
2923D ALA* 1.3 61.5 + - - +
2925D GLU* 3.6 5.4 + - - +
2926D LEU* 3.4 20.8 + - - +
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Residues in contact with ALA2923 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2875D ALA* 3.4 35.7 - - + +
2878D LEU* 3.9 21.5 - - + +
2879D ALA* 3.9 4.3 - - + +
2919D ASP 3.4 13.5 + - - +
2920D ARG* 4.0 3.4 - - - +
2921D GLU 3.3 0.4 - - - -
2922D LYS* 1.3 77.5 - - - +
2924D GLN* 1.3 64.3 + - - +
2926D LEU* 3.4 6.2 + - - +
2927D LEU* 3.2 22.5 + - - +
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Residues in contact with GLN2924 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2875D ALA* 4.9 6.4 - - + +
2920D ARG 2.9 19.0 + - - +
2921D GLU* 4.1 5.6 - - - +
2923D ALA* 1.3 74.5 - - - +
2925D GLU* 1.3 60.1 + - - +
2927D LEU* 3.9 5.4 - - - +
2928D LYS* 2.9 32.1 + - - +
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Residues in contact with GLU2925 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2862D LEU* 6.4 1.6 - - - -
2921D GLU 3.0 18.6 + - - +
2922D LYS* 3.9 7.2 - - - +
2923D ALA 3.3 0.4 - - - -
2924D GLN* 1.3 78.8 - - - +
2926D LEU* 1.3 61.2 - - - +
2928D LYS* 4.1 4.2 - - - +
2929D PHE* 3.2 24.3 + - - +
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Residues in contact with LEU2926 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2812D SER* 5.4 12.1 - - - -
2922D LYS 3.4 13.3 + - - +
2923D ALA* 3.9 6.3 - - - +
2924D GLN 3.3 0.4 - - - -
2925D GLU* 1.3 77.7 - - - +
2927D LEU* 1.3 63.4 + - - +
2929D PHE* 3.6 4.5 + - - +
2930D LEU* 3.3 23.2 + - - +
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Residues in contact with LEU2927 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2871D LEU* 5.3 18.6 - - + +
2875D ALA* 5.6 4.0 - - + -
2923D ALA 3.2 17.0 + - - +
2924D GLN* 4.0 5.4 - - - +
2926D LEU* 1.3 74.0 - - - +
2928D LYS* 1.3 65.6 + - - +
2930D LEU* 3.4 5.3 + - - +
2931D GLN* 3.1 24.8 + - - +
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Residues in contact with LYS2928 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2862D LEU* 4.5 17.5 - - + +
2865D VAL* 4.2 26.4 - - + +
2924D GLN 2.9 18.8 + - - +
2925D GLU* 4.1 5.4 - - - +
2927D LEU* 1.3 77.7 - - - +
2929D PHE* 1.3 60.8 + - - +
2931D GLN* 3.6 4.7 + - - +
2932D MET* 3.1 23.7 + - - +
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Residues in contact with PHE2929 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2758D PHE* 5.2 16.4 - - + -
2925D GLU 3.2 18.9 + - - +
2926D LEU* 3.6 5.6 + - - +
2928D LYS* 1.3 78.4 - - - +
2930D LEU* 1.3 61.5 + - - +
2932D MET* 3.6 6.1 + - - +
2933D ASN* 3.4 22.0 + - - +
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Residues in contact with LEU2930 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2926D LEU 3.3 17.9 + - - +
2927D LEU* 3.9 6.1 - - - +
2928D LYS 3.3 0.2 - - - -
2929D PHE* 1.3 75.0 - - - +
2931D GLN* 1.3 62.0 + - - +
2933D ASN* 3.3 8.2 + - - -
2935D TYR* 2.8 48.4 + - + +
2937D VAL* 5.9 7.0 - - + -
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Residues in contact with GLN2931 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2927D LEU 3.1 17.2 + - - +
2928D LYS* 4.1 5.4 - - - +
2930D LEU* 1.3 77.4 - - - +
2932D MET* 1.3 62.2 + - - +
2934D GLY* 3.3 10.8 + - - -
2935D TYR 4.0 9.6 + - - +
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Residues in contact with MET2932 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2828D GLU 4.5 0.9 - - - +
2829D GLY* 3.4 2.1 - - - -
2830D GLU* 2.9 38.0 + - + +
2928D LYS 3.1 18.1 + - - +
2929D PHE* 3.9 7.4 - - - +
2930D LEU 3.2 0.2 - - - -
2931D GLN* 1.3 78.3 - - - +
2933D ASN* 1.3 55.4 + - - +
2934D GLY 3.2 1.0 + - - -
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Residues in contact with ASN2933 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2754D PHE* 6.2 4.0 - - + -
2825D LYS* 5.3 4.0 - - - +
2827D ARG 3.6 7.1 - - - +
2829D GLY* 3.7 18.0 + - - -
2929D PHE 3.4 12.2 + - - +
2930D LEU* 3.3 6.8 + - - +
2931D GLN 3.3 0.6 - - - -
2932D MET* 1.3 77.4 - - - +
2934D GLY* 1.3 59.2 + - - +
2935D TYR* 3.4 4.0 - - + +
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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
------------------------------------------------------------
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