Contacts of the helix formed by residues 2627 - 2638 (chain B) in PDB entry 5NUG
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 THR2627 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2625B ALA 5.4 0.9 - - - -
2626B THR* 1.3 96.9 - - - +
2628B PRO* 1.3 65.0 - - - +
2629B GLU* 2.7 41.3 + - - +
2630B LEU* 2.9 21.5 + - - +
2631B LEU* 5.4 0.6 - - - +
2678B ARG* 3.7 32.1 - - + +
2679B VAL* 3.3 8.1 - - - -
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Residues in contact with PRO2628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2258B ALA 3.6 12.6 - - - +
2627B THR* 1.3 84.2 - - - +
2629B GLU* 1.3 56.6 + - - +
2630B LEU 3.2 0.2 - - - -
2631B LEU* 3.2 15.5 + - + +
2632B LEU* 2.9 35.4 + - + +
2678B ARG* 4.0 19.5 - - + +
2679B VAL* 3.7 17.0 - - + +
2682B PHE* 3.5 51.8 - - + -
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Residues in contact with GLU2629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2263B HIS* 5.3 9.3 - - + -
2627B THR* 2.7 23.5 + - - +
2628B PRO* 1.3 74.1 - - - +
2630B LEU* 1.3 55.9 + - - +
2632B LEU* 3.2 12.2 + - + +
2633B LYS* 2.9 52.5 + - - +
2678B ARG* 5.6 4.9 + - - +
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Residues in contact with LEU2630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2620B LEU* 4.4 12.6 - - + -
2621B ASN 4.6 5.4 - - - +
2622B PHE* 4.1 29.2 - - + -
2626B THR* 4.2 13.2 - - + -
2627B THR 2.9 17.8 + - - +
2629B GLU* 1.3 73.5 - - - +
2631B LEU* 1.3 59.9 + - + +
2633B LYS* 3.2 13.5 + - + +
2634B THR* 2.9 36.4 + - - +
3006B GLU* 3.7 26.9 - - + +
3010B THR* 4.8 8.5 - - + +
3018B PRO* 4.8 21.8 - - + +
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Residues in contact with LEU2631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2620B LEU* 3.5 26.2 - - + -
2622B PHE* 4.2 13.7 - - + -
2627B THR 5.4 0.2 - - - +
2628B PRO* 3.2 12.1 + - + +
2630B LEU* 1.3 78.7 - - + +
2632B LEU* 1.3 57.1 + - - +
2634B THR* 3.2 6.0 + - - -
2635B PHE* 2.9 44.8 + - + -
2661B LEU* 3.7 24.0 - - + -
2663B CYS* 4.7 1.3 - - - -
2679B VAL* 4.2 17.7 - - + -
2682B PHE* 3.8 19.1 - - + -
2683B ILE* 3.6 28.9 - - + -
2686B MET* 5.0 0.2 - - - -
2708B PHE* 4.5 6.5 - - + -
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Residues in contact with LEU2632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2628B PRO* 2.9 26.1 + - + +
2629B GLU* 3.4 14.6 - - + +
2631B LEU* 1.3 77.4 - - - +
2633B LYS* 1.3 57.2 + - + +
2635B PHE* 3.2 9.7 + - + +
2636B ASP* 2.9 38.3 + - - +
2641B TYR* 4.4 12.5 + - - +
2682B PHE* 3.5 31.4 - - + -
2692B PHE* 4.3 16.8 - - + -
2693B TYR 5.5 1.8 - - - +
2694B ARG* 5.5 5.2 - - + -
2695B THR* 4.6 20.2 - - - +
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Residues in contact with LYS2633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2629B GLU* 2.9 38.2 + - - +
2630B LEU* 3.4 13.8 - - + +
2632B LEU* 1.3 75.5 - - + +
2634B THR* 1.3 58.5 + - - +
2636B ASP* 3.2 12.0 + - - +
2637B HIS* 2.9 27.9 + - - +
3007B ARG* 3.7 23.6 - - - +
3018B PRO* 4.0 18.6 - - + +
3019B GLY* 3.9 34.0 + - - +
3022B GLU* 6.0 3.1 - - - +
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Residues in contact with THR2634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2618B VAL* 3.5 32.1 - - + -
2620B LEU* 3.5 23.6 - - + +
2630B LEU* 2.9 14.7 + - - +
2631B LEU* 3.4 10.3 - - - -
2633B LYS* 1.3 77.0 - - - +
2635B PHE* 1.3 57.7 + - + +
2637B HIS* 3.2 3.2 + - - -
2638B TYR* 2.9 37.5 + - + +
2661B LEU* 4.6 14.6 - - + -
3018B PRO* 3.9 21.1 - - + +
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Residues in contact with PHE2635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2631B LEU* 2.9 31.3 + - + -
2632B LEU* 3.2 11.0 + - + +
2634B THR* 1.3 77.6 - - + +
2636B ASP* 1.3 57.2 + - - +
2638B TYR* 5.0 0.2 - - - -
2639B CYS* 2.5 46.1 + - - +
2641B TYR* 4.5 4.3 - - - +
2650B LEU* 3.5 32.1 - - + -
2659B LEU* 4.8 3.4 - - + -
2661B LEU* 3.3 35.0 - - + -
2682B PHE* 4.7 2.5 - + - -
2686B MET* 3.4 39.0 - - + -
2692B PHE* 4.2 9.6 - + - -
2706B ILE* 3.4 27.8 - - + -
2708B PHE* 4.2 2.2 - + - -
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Residues in contact with ASP2636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2632B LEU* 2.9 22.4 + - - +
2633B LYS* 3.4 12.2 - - - +
2635B PHE* 1.3 76.0 - - - +
2637B HIS* 1.3 62.7 + - - +
2639B CYS 3.3 14.9 - - - +
2640B GLU* 5.4 0.9 - - - +
2641B TYR* 3.5 29.1 + - - -
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Residues in contact with HIS2637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2633B LYS 2.9 12.8 + - - +
2634B THR* 3.2 9.6 + - - +
2636B ASP* 1.3 80.1 - - - +
2638B TYR* 1.3 91.3 + + + +
2639B CYS 3.9 0.3 + - - +
2653B VAL* 5.3 4.0 - - - +
3016B GLU* 4.8 0.7 - - - -
3018B PRO* 5.4 11.0 - - + -
3019B GLY 5.6 2.0 - - - +
3026B TYR* 3.4 28.9 + + - -
3048B GLU* 3.9 28.0 - - - +
3051B TYR* 3.2 48.9 - + + -
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Residues in contact with TYR2638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2616B GLU* 4.5 12.1 - - - -
2617B VAL 4.9 1.1 + - - -
2618B VAL* 3.4 42.9 - - + +
2634B THR* 2.9 32.3 + - + +
2637B HIS* 1.3 103.6 + + + +
2639B CYS* 1.3 65.8 + - - +
2652B PRO* 3.5 3.8 - - - +
2653B VAL* 3.4 20.9 + - - +
2659B LEU* 3.9 25.4 - - + +
3016B GLU* 3.4 27.9 + - - -
3018B PRO* 5.7 5.4 - - + -
3048B GLU* 3.8 24.4 + - - -
3051B TYR* 5.8 0.2 - - - -
3052B LYS* 4.7 12.7 + - - -
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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
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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