Contacts of the helix formed by residues 6 - 18 (chain C) in PDB entry 4NFT
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 TYR 6 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C SER* 1.3 80.5 - - - +
7C SER* 1.3 66.9 + - - +
8C ILE 3.1 3.4 - - - -
9C TYR* 2.8 33.9 + + + -
10C VAL* 3.0 14.2 + - + +
32C ASN* 2.8 12.3 + - - +
35C VAL* 3.9 37.9 - - + -
36C ASN* 3.6 29.6 - - - -
39C PHE* 4.0 26.3 - + - -
107C PHE* 4.4 7.4 - + + -
108C PRO* 3.9 24.5 - - + -
111C ARG* 4.2 20.0 + - - +
112C ILE* 4.0 15.5 - - + +
115C HIS* 5.4 2.3 - - - +
138C LEU* 5.6 0.9 - - + -
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Residues in contact with SER 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C SER* 3.6 12.1 + - - -
6C TYR* 1.3 76.2 - - - +
8C ILE* 1.3 61.5 + - - +
10C VAL* 3.3 2.9 + - - +
11C TYR* 3.0 19.8 + - - +
28C MET* 3.4 45.3 + - - +
29C GLY* 5.6 0.5 - - - -
32C ASN* 3.8 17.0 + - - +
11D TYR* 6.3 0.7 - - - -
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Residues in contact with ILE 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C SER* 5.3 1.5 + - - +
6C TYR* 2.9 2.5 + - - -
7C SER* 1.3 77.6 - - - +
9C TYR* 1.3 92.2 + - + +
11C TYR* 3.4 5.3 + - + +
12C LYS* 3.1 29.3 + - + +
8D ILE* 3.9 27.4 - - + +
11D TYR* 4.0 21.3 - - + -
12D LYS* 3.8 44.0 - - + +
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Residues in contact with TYR 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 2.8 22.4 + + + +
8C ILE* 1.3 93.8 - - + +
10C VAL* 1.3 66.0 + - - +
12C LYS* 3.2 19.6 + - + +
13C VAL* 3.1 26.3 + - - +
106C GLN* 3.2 21.6 - - - +
107C PHE* 4.0 24.4 - - + -
108C PRO* 3.6 38.1 - - + +
111C ARG* 3.4 34.6 + - - -
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Residues in contact with VAL 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR 3.0 16.1 + - - +
7C SER* 3.6 7.0 - - - +
9C TYR* 1.3 76.7 - - - +
11C TYR* 1.3 63.1 + - - +
13C VAL* 3.3 3.5 + - - +
14C LEU* 2.9 22.4 + - + +
23C ILE* 5.0 1.8 - - + -
28C MET* 3.8 20.9 - - + -
31C MET* 4.1 25.8 - - + +
32C ASN 5.1 0.7 - - - +
35C VAL* 4.2 24.9 - - + -
107C PHE* 4.6 3.4 - - + -
142C THR* 4.2 14.8 - - + -
146C LEU* 3.7 22.8 - - + +
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Residues in contact with TYR 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER 3.0 13.5 + - - +
8C ILE* 3.5 10.3 - - + +
9C TYR 3.2 0.2 - - - -
10C VAL* 1.3 77.3 - - - +
12C LYS* 1.3 62.1 + - - +
14C LEU* 3.4 17.5 + - + +
15C LYS* 3.0 70.1 + - + +
22C GLY* 5.1 5.6 - - - -
23C ILE* 4.6 7.9 - - + -
28C MET* 4.0 5.8 - - + +
7D SER 5.7 0.7 - - - -
8D ILE* 4.0 16.2 - - + -
11D TYR* 3.5 70.0 - + + -
23D ILE* 4.5 13.5 + - - +
28D MET* 4.7 6.7 - - + +
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Residues in contact with LYS 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.1 21.4 + - + +
9C TYR* 3.2 21.9 + - + +
11C TYR* 1.3 77.2 - - - +
13C VAL* 1.3 61.4 + - - +
15C LYS* 3.2 17.1 + - - +
16C GLN* 3.3 14.4 + - - +
106C GLN* 3.4 45.3 + - + +
8D ILE* 3.7 35.2 - - + +
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Residues in contact with VAL 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR 3.1 13.9 + - - +
10C VAL 3.3 6.0 + - - +
12C LYS* 1.3 74.4 - - - +
14C LEU* 1.3 59.1 + - - +
16C GLN* 2.8 33.0 + - + +
17C VAL* 3.2 11.0 + - + +
106C GLN* 4.0 17.3 - - + -
107C PHE* 3.8 21.5 - - + -
139C GLU* 4.1 14.8 - - + +
142C THR* 4.2 3.1 - - + -
143C ALA* 3.6 40.6 - - + +
146C LEU* 4.0 8.1 - - + -
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 2.9 17.8 + - + +
11C TYR* 3.6 15.3 - - + +
13C VAL* 1.3 76.8 - - - +
15C LYS* 1.3 58.6 + - - +
17C VAL* 4.1 8.7 - - + -
18C HIS* 2.9 47.3 + - + +
21C THR* 3.7 25.4 - - + +
22C GLY* 4.1 4.7 - - - +
23C ILE* 3.9 36.3 - - + -
146C LEU* 3.6 15.4 - - + +
161C ILE* 4.0 23.1 - - + -
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C TYR* 3.0 65.2 + - + +
12C LYS* 3.2 10.0 + - - +
14C LEU* 1.3 78.2 - - - +
16C GLN* 1.3 61.7 + - + +
18C HIS 4.1 2.2 - - - -
19C PRO* 3.1 46.3 + - - +
20C ASP 4.5 0.8 - - - -
21C THR 2.8 33.2 + - - +
22C GLY* 4.4 1.6 - - - -
8D ILE* 6.3 0.4 - - + -
23D ILE 4.8 7.7 + - - -
25D SER* 5.9 1.6 - - - +
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Residues in contact with GLN 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ARG* 2.8 23.7 + - - -
12C LYS 3.3 12.4 + - - +
13C VAL* 2.8 15.4 + - + +
15C LYS* 1.3 81.1 - - - +
17C VAL* 1.3 61.3 + - + +
19C PRO* 4.5 2.5 - - - +
106C GLN* 2.9 40.2 - - - +
139C GLU* 5.0 3.8 - - - +
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 3.3 22.3 + - - +
13C VAL* 3.7 12.3 - - + +
14C LEU* 3.7 14.6 - - + +
16C GLN* 1.3 84.0 - - + +
18C HIS* 1.3 91.4 + - + +
143C ALA* 4.4 25.8 - - + +
146C LEU* 4.2 7.2 - - + -
147C GLU* 4.2 30.1 - - + +
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Residues in contact with HIS 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 2.9 22.4 + - + +
15C LYS* 4.1 0.9 - - - -
17C VAL* 1.3 97.4 + - + +
19C PRO* 1.3 69.9 - - - +
20C ASP 3.3 2.7 - - - -
21C THR* 3.1 32.7 + - - +
146C LEU 3.6 11.9 - - - -
147C GLU* 3.0 26.3 + - + +
150C GLY* 3.5 28.1 - - - -
151C ASN* 3.4 19.7 + - - -
154C LYS* 3.1 33.7 + - - +
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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