Contacts of the helix formed by residues 13 - 28 (chain B) in PDB entry 5GKI
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 SER 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B SER 4.0 0.2 + - - -
12B PRO* 1.3 74.8 - - - +
14B THR* 1.3 62.6 + - - +
15B GLU* 2.9 19.7 + - - +
16B GLU* 2.9 27.0 + - - -
17B LEU* 2.8 28.0 + - - +
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Residues in contact with THR 14 (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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12B PRO 4.0 0.6 + - - -
13B SER* 1.3 74.9 + - - +
15B GLU* 1.3 63.1 + - - +
17B LEU* 3.2 8.0 + - + +
18B VAL* 3.0 31.5 + - + +
88B LEU* 4.1 28.3 - - + +
92B PRO* 4.5 14.3 - - + +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 2.9 11.6 + - - +
14B THR* 1.3 81.6 - - - +
16B GLU* 1.3 59.2 + - + +
18B VAL* 3.8 4.8 - - - +
19B SER* 2.9 31.7 + - - -
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.6 32.5 - - + +
10B THR 5.1 0.2 - - - +
11B SER 4.6 1.7 - - - +
12B PRO* 3.5 16.0 - - + +
13B SER* 2.9 38.0 + - - +
15B GLU* 1.3 75.1 - - + +
17B LEU* 1.3 66.6 + - - +
19B SER* 3.1 7.4 + - - -
20B LEU* 2.9 28.0 + - - +
115B VAL* 5.3 0.7 - - - -
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PRO* 4.3 5.0 - - + +
13B SER 2.8 12.7 + - - +
14B THR* 3.4 13.0 - - + +
16B GLU* 1.3 77.5 - - - +
18B VAL* 1.3 55.0 + - + +
20B LEU* 3.1 1.0 + - - +
21B VAL* 2.8 57.2 + - + +
33B ILE* 4.6 7.6 - - + -
86B LEU* 4.3 7.4 - - + -
92B PRO* 3.6 37.9 - - + -
109B LEU* 4.4 5.8 - - + -
112B VAL* 4.1 29.6 - - + -
115B VAL* 4.3 24.2 - - + -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 3.0 20.8 + - + +
15B GLU* 3.8 5.4 - - - +
17B LEU* 1.3 80.3 - - + +
19B SER* 1.3 66.0 + - - +
22B ASN* 3.0 44.9 + - - +
86B LEU* 3.9 23.6 - - + -
88B LEU* 3.7 30.3 - - + -
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLU* 2.9 22.9 + - - -
16B GLU* 3.3 9.2 - - - -
17B LEU 3.1 0.2 - - - -
18B VAL* 1.3 78.0 - - - +
20B LEU* 1.3 63.8 + - - +
22B ASN* 4.0 1.7 - - - +
23B SER* 3.0 29.2 + - - -
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B THR* 3.9 31.0 - - + +
9B ILE* 3.9 28.9 - - + -
16B GLU 2.9 15.2 + - - +
17B LEU 3.7 2.2 - - - +
19B SER* 1.3 81.4 - - - +
21B VAL* 1.3 60.6 + - - +
23B SER* 3.0 7.0 + - - -
24B ALA* 2.8 30.1 + - - +
31B LEU* 4.9 0.4 - - - -
115B VAL* 3.6 46.9 - - + +
116B SER 4.3 0.9 - - - +
117B VAL* 3.7 17.1 - - + +
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Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 2.8 48.3 + - + +
18B VAL 4.1 2.0 - - - +
20B LEU* 1.3 70.6 - - - +
22B ASN* 1.3 64.1 + - - +
24B ALA* 3.0 13.3 + - - +
25B LEU* 3.1 27.6 + - + +
31B LEU* 4.1 29.6 - - + -
33B ILE* 4.5 4.9 - - + -
86B LEU* 4.0 30.5 - - + -
94B LEU* 4.3 13.0 - - + -
109B LEU* 6.1 0.4 - - + -
115B VAL* 4.5 3.1 - - + -
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Residues in contact with ASN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 3.0 40.9 + - - +
19B SER* 4.2 1.6 - - - +
21B VAL* 1.3 83.1 - - - +
23B SER* 1.3 61.8 + - - +
25B LEU* 3.6 15.2 + - - +
26B LEU* 3.1 40.3 + - + +
86B LEU* 4.5 13.4 + - - +
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Residues in contact with SER 23 (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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3B LYS* 4.3 1.2 + - - -
19B SER* 3.0 19.3 + - - -
20B LEU* 3.0 9.9 + - - -
22B ASN* 1.3 79.2 - - - +
24B ALA* 1.3 56.1 + - - +
26B LEU* 4.7 4.7 - - - -
27B GLU* 2.5 66.8 + - - +
117B VAL* 5.3 3.4 - - - -
119B ARG* 4.6 3.9 + - - -
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Residues in contact with ALA 24 (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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20B LEU 2.8 11.9 + - - +
21B VAL 3.0 8.7 + - - +
23B SER* 1.3 76.9 - - - +
25B LEU* 1.3 55.8 + - + +
27B GLU* 3.2 2.1 + - - -
28B GLU* 2.8 30.7 + - - -
29B ALA 3.3 16.2 + - - +
31B LEU* 3.9 33.0 - - + -
117B VAL* 4.0 23.5 - - + +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 3.1 29.8 + - + +
22B ASN* 3.9 17.0 - - - +
24B ALA* 1.3 80.3 - - + +
26B LEU* 1.3 70.6 + - + +
28B GLU* 3.5 16.2 + - - +
29B ALA 6.0 0.7 - - - +
31B LEU* 5.2 4.7 - - + -
58B VAL* 4.3 25.4 - - + -
84B VAL* 3.6 37.7 - - + +
85B ARG* 4.5 6.7 - - - +
86B LEU 4.8 1.3 - - - +
94B LEU* 5.7 0.7 - - + -
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASN* 3.1 28.8 + - + +
23B SER* 4.1 4.0 - - - +
25B LEU* 1.3 86.6 - - + +
27B GLU* 1.3 62.4 + - + +
28B GLU* 3.1 10.1 + - - +
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Residues in contact with GLU 27 (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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3B LYS* 2.5 38.5 + - - +
23B SER* 2.5 43.1 + - - +
24B ALA* 4.1 1.8 - - - +
26B LEU* 1.3 71.9 - - + +
28B GLU* 1.3 73.9 + - - +
29B ALA* 4.4 8.3 - - + +
117B VAL* 5.1 1.5 - - - +
119B ARG* 2.7 36.2 + - + +
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Residues in contact with GLU 28 (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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24B ALA 2.8 8.6 + - - -
25B LEU* 3.9 12.6 - - - +
26B LEU 3.1 7.7 - - - +
27B GLU* 1.3 83.5 - - - +
29B ALA* 1.3 56.6 + - - +
60B PRO* 3.1 46.6 - - + +
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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