Contacts of the helix formed by residues 12 - 25 (chain B) in PDB entry 4HI7
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 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B ILE* 3.1 24.8 + - - +
10B ASP 3.1 1.2 - - - -
11B ALA* 1.3 77.0 - - - +
13B PRO* 1.3 68.3 - - - +
14B PRO* 3.3 12.0 - - - +
15B VAL* 3.5 16.6 - - - +
16B ARG* 3.1 21.8 + - - +
36B LEU* 5.0 1.3 - - - -
55B VAL* 4.2 1.9 - - - +
301B GSH 3.3 31.2 - - - +
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Residues in contact with PRO 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA 3.4 8.1 - - - +
12B SER* 1.3 82.6 - - - +
14B PRO* 1.3 73.0 - - + +
16B ARG* 3.0 22.4 + - - +
17B ALA 3.1 0.5 + - - -
103B GLU* 5.6 0.4 - - - +
108B PHE* 4.4 3.1 - - + -
112B LEU* 3.8 24.9 - - + -
166B SER* 3.1 42.4 - - - +
167B SER* 4.1 6.7 - - - +
170B SER* 3.4 18.4 - - - +
208B PHE* 4.5 9.2 - - + -
301B GSH 4.2 8.7 - - - -
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Residues in contact with PRO 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B SER* 3.3 14.4 - - - +
13B PRO* 1.3 97.3 - - + +
15B VAL* 1.3 60.1 + - - +
17B ALA* 3.3 11.3 + - + +
18B VAL* 3.4 10.2 + - - +
55B VAL 3.9 5.4 - - - +
56B PRO* 3.6 18.6 - - + -
68B SER* 3.4 32.0 - - - +
103B GLU* 6.1 0.9 - - - +
108B PHE* 3.7 15.3 - - + -
166B SER* 4.5 1.6 - - - +
301B GSH 3.6 29.8 - - + +
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Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 4.4 6.7 - - + +
8B GLY* 3.7 24.0 - - - -
9B ILE 3.5 21.5 - - - +
10B ASP* 4.9 0.2 - - - -
12B SER* 3.2 21.5 + - - +
13B PRO 3.2 0.6 - - - -
14B PRO* 1.3 78.8 - - - +
16B ARG* 1.3 57.5 + - - +
18B VAL* 3.1 6.1 + - - +
19B LYS* 2.9 35.4 + - + +
31B TYR* 3.7 21.3 - - + +
55B VAL* 3.9 3.1 - - + -
56B PRO* 3.7 28.5 - - + -
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 2.8 32.0 + - + +
11B ALA 2.9 21.2 + - - -
12B SER 3.1 5.7 + - - -
13B PRO* 3.0 21.1 + - - +
15B VAL* 1.3 74.3 - - - +
17B ALA* 1.3 64.5 + - - +
19B LYS* 3.7 9.1 - - + +
20B LEU* 2.9 29.4 + - - +
166B SER* 3.1 19.6 + - - -
169B SER* 3.5 7.1 + - - -
170B SER* 2.8 22.0 + - - -
200B GLU 3.5 13.4 - - - +
201B ASN* 2.8 60.1 + - - +
204B GLY* 3.5 3.6 - - - -
205B ALA* 3.4 23.0 - - - +
208B PHE* 4.0 3.8 - - - +
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Residues in contact with ALA 17 (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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13B PRO 3.1 6.4 + - - +
14B PRO* 3.6 11.9 - - + +
15B VAL 3.3 0.4 - - - -
16B ARG* 1.3 76.1 - - - +
18B VAL* 1.3 60.2 + - - +
20B LEU* 3.4 4.4 + - - +
21B THR* 2.9 26.2 + - - -
68B SER* 4.7 2.2 - - - +
72B MET* 3.5 23.2 - - + +
162B PHE* 3.7 20.3 - - - +
163B SER* 3.9 7.6 - - - +
166B SER* 3.6 19.2 - - - +
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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
----------------------------------------------------------
6B LEU* 3.8 26.0 - - + -
14B PRO 3.4 12.5 + - - +
15B VAL* 3.1 8.4 + - - +
17B ALA* 1.3 75.4 - - - +
19B LYS* 1.3 59.0 + - - +
21B THR* 3.1 2.1 + - - -
22B LEU* 2.9 41.7 + - + +
56B PRO* 4.0 8.5 - - + -
58B LEU* 5.1 0.4 - - + -
68B SER* 3.9 23.8 - - - +
71B ILE* 3.9 31.0 - - + -
72B MET* 4.2 8.1 - - + -
75B LEU* 4.2 6.1 - - + -
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.9 17.0 - - + -
10B ASP* 2.7 38.0 + - - +
15B VAL* 2.9 23.1 + - + +
16B ARG* 3.2 11.4 + - + +
18B VAL* 1.3 74.7 - - - +
20B LEU* 1.3 62.9 + - - +
22B LEU* 3.4 4.5 + - - +
23B ALA* 3.0 24.3 + - - +
29B TYR* 3.9 13.0 + - - +
31B TYR* 3.6 22.8 - - + +
200B GLU* 3.2 52.8 + - + +
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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
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16B ARG 2.9 18.9 + - - +
17B ALA* 3.6 6.7 - - - +
19B LYS* 1.3 76.5 - - - +
21B THR* 1.3 58.3 + - - +
23B ALA* 3.3 5.7 + - - +
24B ALA* 2.9 29.1 + - - +
162B PHE* 3.8 32.3 - - + +
165B ILE* 3.7 30.3 - - + -
166B SER 5.3 0.2 - - - +
195B LEU* 5.5 1.8 - - + -
197B TYR* 3.7 36.8 - - + +
198B TYR* 4.4 10.5 - - + -
200B GLU* 4.2 1.1 - - + -
201B ASN* 3.9 31.6 - - + +
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Residues in contact with THR 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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17B ALA 2.9 12.7 + - - -
18B VAL* 3.1 9.2 + - - -
20B LEU* 1.3 74.8 - - - +
22B LEU* 1.3 65.4 + - - +
24B ALA* 3.2 1.9 + - - +
25B LEU* 3.0 46.2 + - + +
72B MET* 3.1 33.8 - - + +
75B LEU* 4.4 7.6 - - + -
76B VAL* 4.1 18.6 - - + -
85B LEU* 5.2 0.7 - - + -
159B ILE* 4.0 7.8 - - + +
162B PHE* 3.3 18.4 - - + -
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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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4B PRO* 4.8 2.7 - - + -
6B LEU* 4.1 9.2 - - + -
18B VAL* 2.9 35.4 + - + +
19B LYS 3.8 2.2 - - - +
21B THR* 1.3 75.2 - - - +
23B ALA* 1.3 57.4 + - - +
25B LEU* 3.4 4.6 + - + +
26B GLN* 3.0 21.7 + - - -
27B LEU* 3.1 41.7 + - + +
29B TYR* 3.5 59.7 - - + -
58B LEU* 5.0 3.6 - - + -
75B LEU* 3.8 26.0 - - + -
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Residues in contact with ALA 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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19B LYS 3.0 17.1 + - - +
20B LEU 3.5 4.7 - - - +
22B LEU* 1.3 75.1 - - - +
24B ALA* 1.3 67.4 + - - +
26B GLN* 3.1 19.7 + - - +
29B TYR* 5.3 0.9 - - - -
197B TYR* 3.6 36.3 - - + -
200B GLU* 4.2 11.9 - - + -
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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 2.9 15.7 + - - +
21B THR 3.2 4.9 + - - +
23B ALA* 1.3 76.7 - - - +
25B LEU* 1.3 62.2 + - - +
26B GLN* 3.2 9.2 + - - +
85B LEU* 3.9 16.0 - - + +
162B PHE* 3.8 15.3 - - + -
197B TYR* 3.4 32.5 - - - +
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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 THR* 3.0 28.0 + - + +
22B LEU* 3.8 7.6 - - - +
23B ALA 3.2 0.2 - - - -
24B ALA* 1.3 76.6 - - - +
26B GLN* 1.3 68.4 + - - +
27B LEU* 3.1 16.5 + - + +
75B LEU* 3.8 39.0 - - + +
76B VAL* 4.2 6.3 - - + +
79B TYR* 4.6 11.1 - - + +
80B GLY* 3.7 28.9 - - - +
81B LYS 5.0 1.1 - - - +
85B LEU* 4.0 21.5 - - + -
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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