Contacts of the helix formed by residues 31 - 41 (chain A) in PDB entry 2G8N
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 GLU 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ARG 3.6 9.0 - - - +
30A PHE* 1.3 74.5 - - - +
32A PRO* 1.3 69.0 - - - +
33A ARG* 3.3 2.5 - - + +
34A ALA* 3.0 14.9 + - + +
35A TYR* 2.9 20.4 + - - +
224A ALA 3.0 14.2 + - - +
225A GLY* 3.5 7.0 - - - -
226A GLU* 2.6 46.3 + - - +
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Residues in contact with PRO 32 (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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30A PHE* 3.3 20.1 - - + +
31A GLU* 1.3 82.0 - - - +
33A ARG* 1.3 59.5 + - + +
35A TYR* 3.0 3.0 + - + +
36A LEU* 2.8 35.4 + - - +
82A PRO* 4.1 13.5 - - + -
105A VAL* 3.9 30.7 - - + +
106A ASN* 3.3 25.4 - - - +
109A GLU* 4.2 16.8 - - + +
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Residues in contact with ARG 33 (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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31A GLU* 3.3 1.9 - - + -
32A PRO* 1.3 78.1 - - + +
34A ALA* 1.3 57.7 + - - +
36A LEU* 3.4 11.5 + - - +
37A ARG* 3.0 31.0 + - - +
109A GLU* 3.0 38.8 + - - +
119A GLY 3.0 21.8 + - - -
120A ALA 5.1 0.6 + - - -
121A PHE* 3.6 32.3 - - - +
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Residues in contact with ALA 34 (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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31A GLU* 3.0 17.8 + - + +
33A ARG* 1.3 75.3 - - - +
35A TYR* 1.3 59.8 + - - +
37A ARG* 3.4 9.5 + - - +
38A ASN* 2.8 41.9 + - - +
225A GLY* 3.4 35.4 - - - +
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Residues in contact with TYR 35 (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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30A PHE* 3.4 26.0 - + + -
31A GLU 2.9 12.5 + - - +
32A PRO 3.3 7.4 - - - +
34A ALA* 1.3 77.2 - - - +
36A LEU* 1.3 66.1 + - + +
38A ASN* 3.4 4.0 + - - +
39A ASN* 3.0 50.2 + - - +
40A TYR* 3.8 12.6 - + - -
82A PRO* 3.7 23.8 - - + -
83A THR* 4.1 1.3 - - + -
222A TYR* 3.8 24.0 - + - -
223A LEU 4.9 0.4 - - - -
224A ALA* 4.3 7.3 - - + +
2001A F83 3.2 20.6 - - + +
3001A SAH 2.5 60.3 + - + +
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Residues in contact with LEU 36 (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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32A PRO 2.8 24.3 + - - +
33A ARG* 3.6 14.4 - - - +
35A TYR* 1.3 77.0 - - + +
37A ARG* 1.3 57.4 + - - +
40A TYR* 2.6 41.9 + - + +
41A ALA* 3.5 1.6 + - - +
82A PRO* 3.7 40.8 - - + +
83A THR* 4.0 7.6 - - + -
109A GLU* 4.3 9.4 - - + -
121A PHE* 3.7 43.3 - - + -
123A TRP* 3.8 21.3 - - + -
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Residues in contact with ARG 37 (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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33A ARG 3.0 18.3 + - - +
34A ALA* 3.7 9.4 - - - +
36A LEU* 1.3 78.9 - - - +
38A ASN* 1.3 74.5 + - - +
39A ASN 3.3 0.5 + - - -
41A ALA* 3.4 32.4 + - + +
42A PRO 4.9 2.1 - - - +
121A PHE* 5.1 1.8 - - - -
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Residues in contact with ASN 38 (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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34A ALA* 2.8 30.8 + - - +
35A TYR* 4.5 0.2 - - - +
36A LEU 3.3 0.2 - - - -
37A ARG* 1.3 92.9 + - - +
39A ASN* 1.3 75.7 + - - +
41A ALA 5.1 1.8 - - - +
44A ARG* 3.8 14.6 - - - +
223A LEU* 3.2 31.7 + - - +
224A ALA* 4.2 2.2 - - - +
225A GLY 4.5 3.4 - - - +
264A THR* 4.9 0.9 + - - -
266A VAL* 3.6 37.7 - - + +
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Residues in contact with ASN 39 (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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35A TYR* 3.0 45.3 + - - -
38A ASN* 1.3 89.0 - - - +
40A TYR* 1.3 75.8 + - + +
41A ALA 3.6 1.3 - - - -
44A ARG* 3.1 42.6 + - - +
222A TYR* 5.2 2.7 - - - +
223A LEU 5.0 2.8 + - - -
266A VAL* 4.1 4.0 - - - +
267A ASP* 4.1 1.7 - - - +
2001A F83 3.0 55.5 + - + +
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Residues in contact with TYR 40 (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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35A TYR* 3.8 6.5 - + - -
36A LEU* 2.6 29.0 + - + +
39A ASN* 1.3 91.1 - - + +
41A ALA* 1.3 58.5 + - - +
42A PRO* 4.9 0.2 - - - +
45A GLY* 3.5 6.1 - - - +
83A THR* 3.7 13.9 - - + -
85A TYR* 3.1 36.5 + + - -
121A PHE* 4.1 14.6 - - + -
123A TRP* 3.9 22.2 - + + -
126A TYR* 2.7 39.5 + + + +
2001A F83 3.4 40.9 - + - -
3001A SAH 2.6 31.0 + - - -
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Residues in contact with ALA 41 (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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36A LEU 3.5 1.2 + - - +
37A ARG* 3.4 33.3 + - + +
38A ASN 5.1 1.2 - - - +
39A ASN 3.6 0.2 - - - -
40A TYR* 1.3 79.9 + - - +
42A PRO* 1.3 81.6 - - + +
43A PRO* 4.4 0.2 - - - +
44A ARG* 3.4 6.1 + - - +
45A GLY* 3.0 14.2 + - - -
121A PHE* 5.5 5.8 - - + -
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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