Contacts of the helix formed by residues 15 - 31 (chain B) in PDB entry 2IHC
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 VAL 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ASN* 3.7 25.6 - - + +
13B SER* 3.5 9.2 - - - +
14B SER* 1.3 83.1 - - - +
16B HIS* 1.3 60.6 + - - +
17B SER 3.5 1.8 - - - -
18B THR* 3.3 7.5 + - - -
19B ASN* 2.9 29.0 + - - +
9C PHE* 4.0 9.4 - - + -
11C TYR* 3.8 22.4 - - + -
119D GLU* 5.1 9.9 - - + -
121D SER* 5.4 4.9 - - - -
122D CYS* 3.8 30.1 - - + +
125D PHE* 4.0 11.7 - - + -
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Residues in contact with HIS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.8 19.1 - - + -
55A CYS* 3.6 21.1 - - + -
90A PHE* 3.4 31.4 + + + -
91A ALA* 2.9 32.5 + - - -
94A ALA* 3.9 11.2 - - + -
116A HIS 4.8 0.9 + - - -
117A ASN* 3.8 22.2 + - + -
13B SER* 3.0 28.1 + - - +
14B SER 3.7 0.8 - - - -
15B VAL* 1.3 75.6 - - - +
17B SER* 1.3 56.1 + - - +
19B ASN* 3.0 3.8 + - - +
20B VAL* 2.8 48.3 + - + +
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Residues in contact with SER 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 2.7 45.6 + - - +
18A THR* 3.4 15.9 + - - -
21A LEU* 4.2 19.2 - - - +
94A ALA* 5.1 5.2 - - - +
13B SER 5.3 0.6 + - - -
14B SER 5.1 4.7 + - - -
15B VAL 3.5 0.4 - - - -
16B HIS* 1.3 78.4 - - - +
18B THR* 1.3 68.7 + - - +
20B VAL* 3.1 7.7 + - - +
21B LEU* 3.0 20.8 + - - +
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Residues in contact with THR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 3.5 17.1 + - - -
14B SER 5.0 2.0 + - - -
15B VAL* 3.3 9.7 + - - -
17B SER* 1.3 82.5 + - - +
19B ASN* 1.3 57.8 + - - +
21B LEU* 3.7 2.7 + - - +
22B LEU* 3.1 30.2 + - + +
0C MET* 3.6 31.6 - - + +
9C PHE* 4.2 11.9 - - + -
125D PHE* 3.8 29.2 - - + -
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Residues in contact with ASN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 3.0 34.7 + - - +
15B VAL* 2.9 13.1 + - - +
16B HIS 3.4 8.3 - - - +
18B THR* 1.3 77.7 - - - +
20B VAL* 1.3 62.6 + - - +
22B LEU* 3.4 11.8 + - - +
23B SER* 2.9 30.3 + - - +
121D SER* 5.2 4.9 - - - -
125D PHE* 3.1 35.9 - - - -
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 6.5 0.2 - - + -
21A LEU* 3.8 25.1 - - + -
24A LEU* 5.1 1.1 - - + -
51A VAL* 4.6 13.9 - - + -
54A ALA* 4.6 11.8 - - + +
55A CYS* 3.9 11.4 - - - -
117A ASN* 5.8 0.4 - - - +
16B HIS* 2.8 54.0 + - + +
17B SER 3.6 6.1 - - - +
19B ASN* 1.3 70.3 - - + +
21B LEU* 1.3 67.4 + - + +
23B SER* 3.1 7.0 + - - -
24B LEU* 2.9 42.0 + - + +
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Residues in contact with LEU 21 (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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16A HIS* 3.6 26.2 - - + -
17A SER* 4.0 15.9 - - - +
20A VAL* 4.2 25.4 - - + -
17B SER 3.0 15.4 + - - +
18B THR* 4.1 3.4 - - - +
20B VAL* 1.3 77.7 - - - +
22B LEU* 1.3 57.1 + - - +
24B LEU* 3.3 15.9 + - + +
25B ASN* 2.8 29.3 + - - +
51B VAL* 5.4 1.6 - - + -
91B ALA 3.6 14.6 - - - +
92B TYR* 3.3 33.8 - - + +
93B THR* 3.7 11.0 - - - +
94B ALA* 4.5 1.1 - - + -
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Residues in contact with LEU 22 (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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18B THR* 3.1 25.7 + - + +
19B ASN* 3.4 15.0 - - - +
20B VAL 3.2 0.2 - - - -
21B LEU* 1.3 75.4 - - - +
23B SER* 1.3 58.6 + - - +
25B ASN* 3.2 10.4 + - + +
26B ASP* 2.9 27.9 + - - +
92B TYR 5.1 0.9 - - - -
93B THR* 6.4 2.0 - - + -
0C MET* 5.3 7.4 - - + -
124D GLN 6.0 0.4 - - - +
125D PHE* 3.3 42.8 - - + -
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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
----------------------------------------------------------
54A ALA* 3.6 36.5 + - - +
19B ASN* 2.9 18.4 + - - +
20B VAL 3.1 0.6 + - - -
22B LEU* 1.3 74.0 - - - +
24B LEU* 1.3 60.6 + - - +
26B ASP* 3.2 9.2 + - - +
27B GLN* 2.9 34.8 + - - +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.9 1.6 - - + -
24A LEU* 4.4 13.0 - - + -
50A SER* 3.8 28.5 - - - +
51A VAL* 4.5 6.1 - - + +
54A ALA* 5.2 1.3 - - + -
20B VAL* 2.9 31.8 + - + +
21B LEU* 3.6 20.4 - - + +
23B SER* 1.3 72.9 - - - +
25B ASN* 1.3 61.3 + - - +
27B GLN* 3.4 24.0 + - - +
28B ARG* 2.9 24.6 + - - +
48B HIS* 3.4 14.3 - - + +
51B VAL* 3.8 24.0 - - + -
92B TYR* 3.8 13.0 - - + -
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Residues in contact with ASN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU 2.8 14.1 + - - +
22B LEU* 3.4 13.8 - - + +
24B LEU* 1.3 76.3 - - - +
26B ASP* 1.3 58.4 + - - +
28B ARG* 3.0 32.9 + - - +
29B LYS* 2.9 44.8 + - - +
89B GLN* 4.8 1.8 + - - -
92B TYR* 3.5 24.7 - - - +
93B THR* 3.4 21.6 - - - +
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU 2.9 13.6 + - - +
23B SER* 3.2 12.8 + - - +
25B ASN* 1.3 73.1 - - - +
27B GLN* 1.3 66.6 + - - +
29B LYS* 4.2 7.6 - - - +
30B LYS* 3.0 38.3 + - - +
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Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A SER* 3.1 37.4 + - - +
53A ALA* 4.5 1.8 - - - +
54A ALA* 4.2 11.7 - - - +
60A HIS* 6.0 2.3 + - + -
23B SER* 2.9 25.0 + - - +
24B LEU* 3.4 11.8 - - - +
26B ASP* 1.3 78.4 + - - +
28B ARG* 1.3 56.1 + - - +
30B LYS* 3.6 0.8 - - - -
31B ASP 2.9 9.2 + - - -
32B VAL* 2.8 55.3 + - + +
33B LEU* 3.9 15.8 - - + +
48B HIS* 3.0 21.9 + - - +
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Residues in contact with ARG 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 LEU 2.9 15.0 + - - +
25B ASN* 3.0 30.2 + - - +
27B GLN* 1.3 75.4 - - - +
29B LYS* 1.3 72.1 + - - +
31B ASP* 2.9 20.6 + - - +
34B CYS* 3.7 13.1 - - - -
45B PHE* 5.3 4.9 - - - -
46B ARG* 3.1 33.6 + - + +
47B ALA* 4.5 0.7 - - - -
88B ILE* 4.2 26.6 - - - +
89B GLN* 3.5 37.6 + - - +
92B TYR* 3.7 40.3 - - + +
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Residues in contact with LYS 29 (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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25B ASN* 2.9 47.2 + - - +
26B ASP* 4.2 7.4 - - - +
28B ARG* 1.3 87.7 - - - +
30B LYS* 1.3 60.6 + - + +
31B ASP* 3.2 2.1 + - - +
89B GLN* 5.8 2.9 - - - +
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Residues in contact with LYS 30 (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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26B ASP* 3.0 32.9 + - - +
27B GLN* 4.0 2.7 - - - +
29B LYS* 1.3 75.1 - - + +
31B ASP* 1.3 68.4 + - - +
32B VAL* 3.5 18.7 + - + +
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Residues in contact with ASP 31 (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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27B GLN 2.9 3.6 + - - -
28B ARG 2.9 14.9 + - - +
29B LYS 3.2 2.0 - - - +
30B LYS* 1.3 81.0 - - - +
32B VAL* 1.3 61.3 + - - +
33B LEU 4.3 0.3 + - - -
34B CYS* 4.2 5.0 - - - +
44B ARG* 4.2 8.0 + - - -
46B ARG* 2.5 55.0 + - + +
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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
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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