Contacts of the strand formed by residues 17 - 23 (chain A) in PDB entry 4N1T
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 ARG 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL 4.3 0.2 - - - +
13A LEU* 3.8 1.0 - - - +
14A GLN* 2.8 61.8 + - + +
16A GLN* 1.3 81.4 - - - +
18A VAL* 1.3 62.7 + - - +
105A TRP* 3.5 59.7 - - + +
106A PHE 3.1 15.0 - - - +
107A GLN* 4.0 13.5 - - - +
108A LEU* 3.6 7.3 - - - +
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Residues in contact with VAL 18 (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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11A LEU* 4.5 8.5 - - + -
12A VAL 3.4 16.6 - - - +
13A LEU* 4.1 13.0 - - + -
17A ARG* 1.3 74.3 - - - +
19A LEU* 1.3 72.6 + - - +
20A LEU* 3.8 8.2 + - + -
105A TRP* 3.5 5.5 - - - -
106A PHE* 2.9 43.9 + - + +
108A LEU* 4.1 10.1 - - + -
111A ILE* 4.1 27.8 - - + -
124A PHE* 4.0 24.0 - - + -
127A LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 19 (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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11A LEU* 4.4 6.6 - - - +
12A VAL* 3.0 24.0 + - + +
18A VAL* 1.3 76.4 - - - +
20A LEU* 1.3 70.3 + - - +
34A GLY* 5.1 0.2 - - - -
35A PHE* 3.6 35.0 - - + -
57A SER* 4.4 4.0 - - - -
59A LEU* 3.7 29.4 - - + -
95A PRO* 3.9 19.3 - - + -
103A PRO* 4.1 2.2 - - + -
104A CYS 3.5 31.2 - - - +
105A TRP* 3.6 32.9 - - + +
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Residues in contact with LEU 20 (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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11A LEU* 3.8 19.3 - - + -
18A VAL* 3.8 11.8 + - + -
19A LEU* 1.3 81.5 - - - +
21A GLY* 1.3 60.0 + - - +
32A TRP* 4.0 13.3 - - + -
33A ASN* 3.5 23.8 - - - +
34A GLY 4.0 0.2 - - - +
35A PHE* 3.8 5.8 - - - -
103A PRO* 3.2 3.5 - - - +
104A CYS 2.8 32.6 + - - +
106A PHE* 3.8 21.3 - - + -
111A ILE* 4.7 2.0 - - + -
112A PRO* 3.8 32.3 - - + -
116A MET* 4.0 15.7 - - + -
124A PHE* 4.2 13.0 - - + -
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Residues in contact with GLY 21 (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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20A LEU* 1.3 75.3 - - - +
22A MET* 1.3 62.9 + - - -
23A LYS* 3.6 2.1 + - - +
31A ARG 3.5 1.6 - - - +
32A TRP* 3.4 5.8 - - - -
33A ASN* 2.8 37.7 + - - +
34A GLY 5.1 0.2 - - - +
35A PHE* 3.7 11.6 - - - -
101A MET* 3.6 18.9 - - - +
102A ARG 3.5 6.1 - - - -
103A PRO* 4.0 1.1 - - - -
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Residues in contact with MET 22 (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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21A GLY* 1.3 69.4 - - - -
23A LYS* 1.3 66.0 + - - +
24A LYS* 3.6 7.7 + - + +
30A GLY* 3.3 35.9 - - - +
31A ARG 3.6 8.5 - - - +
32A TRP* 3.4 44.7 - - + +
101A MET* 3.4 3.6 - - - -
102A ARG* 2.9 60.3 + - + +
115A ASP* 3.4 26.2 - - - +
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Residues in contact with LYS 23 (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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21A GLY 3.6 3.2 + - - +
22A MET* 1.3 74.8 - - - +
24A LYS* 1.3 61.1 + - - +
25A ARG 3.2 25.8 - - - +
26A GLY* 4.5 0.9 - - - -
27A PHE* 3.0 38.1 + - - +
28A GLY* 4.0 13.5 - - - +
29A ALA* 3.2 3.2 - - - +
30A GLY* 2.8 30.0 + - - -
31A ARG 3.3 9.4 + - - +
33A ASN* 6.4 1.1 - - + -
100A GLU* 3.7 11.9 - - + +
101A MET* 3.7 19.3 - - + -
201A 2GD 4.6 14.3 - - + -
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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