Contacts of the strand formed by residues 101 - 107 (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 MET 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLY* 3.6 32.8 - - - +
22A MET 3.4 10.5 - - - +
23A LYS* 3.7 23.6 - - + -
24A LYS* 3.9 2.8 - - - +
34A GLY 4.9 6.7 - - - +
35A PHE* 3.8 16.4 - - + -
56A GLU* 3.6 46.0 - - - +
96A VAL 4.2 0.3 - - - +
97A GLU* 3.5 4.0 - - - +
98A SER* 2.9 30.6 + - - +
100A GLU* 1.3 104.1 - - + +
102A ARG* 1.3 61.7 + - - +
103A PRO* 3.5 2.7 - - + +
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Residues in contact with ARG 102 (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* 4.1 0.7 - - - -
22A MET* 2.9 59.8 + - + +
24A LYS* 3.9 9.2 - - - +
32A TRP* 3.3 35.4 - - + -
97A GLU* 3.5 35.9 - - + +
101A MET* 1.3 71.8 - - - +
103A PRO* 1.4 70.3 - - + +
104A CYS* 5.6 4.3 - - + +
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Residues in contact with PRO 103 (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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19A LEU* 4.1 8.1 - - + -
20A LEU 3.2 10.3 - - - +
21A GLY* 4.0 2.0 - - - -
35A PHE* 4.1 12.6 - - + -
56A GLU 4.5 0.7 - - - +
57A SER* 4.4 13.7 - - - +
95A PRO* 3.8 29.2 - - + +
96A VAL 3.4 28.7 - - - +
97A GLU* 3.8 8.2 - - + +
101A MET* 3.5 7.6 - - + +
102A ARG* 1.4 91.0 - - - +
104A CYS* 1.3 62.6 + - - +
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Residues in contact with CYS 104 (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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19A LEU* 3.5 5.8 - - - +
20A LEU 2.8 30.6 + - - +
32A TRP* 3.7 26.2 - - + -
102A ARG* 3.8 4.5 + - + +
103A PRO* 1.3 77.5 - - - +
105A TRP* 1.3 74.0 + - - +
106A PHE* 3.3 17.8 - - + -
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Residues in contact with TRP 105 (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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12A VAL* 3.8 23.6 - - + -
14A GLN* 3.7 24.5 - - + -
17A ARG* 3.5 68.6 - - + +
18A VAL* 3.5 19.3 - - - -
19A LEU* 3.6 31.9 - - + -
59A LEU* 5.3 0.4 - - + -
91A ILE* 4.8 10.5 - - + -
95A PRO* 4.0 25.6 - - + +
104A CYS* 1.3 87.5 - - - +
106A PHE* 1.3 62.7 + - - +
107A GLN* 6.2 0.7 - - - +
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Residues in contact with PHE 106 (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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17A ARG* 3.1 6.4 - - - -
18A VAL* 2.9 44.4 + - + +
20A LEU* 3.8 18.8 - - + -
32A TRP* 3.7 49.8 - + - -
104A CYS* 3.3 29.8 - - + -
105A TRP* 1.3 74.4 - - - +
107A GLN* 1.3 70.7 + - - +
110A GLN* 3.5 22.4 - - + +
111A ILE* 4.7 2.7 - - + -
112A PRO* 3.8 22.2 - - + -
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Residues in contact with GLN 107 (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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16A GLN* 3.4 27.5 + - - +
17A ARG* 4.0 14.5 - - - +
105A TRP* 6.2 0.4 - - - +
106A PHE* 1.3 77.5 - - - +
108A LEU* 1.3 60.5 + - - +
109A ASP* 3.4 18.8 - - - +
110A GLN* 2.9 47.2 + - - +
111A ILE* 3.6 2.1 + - - +
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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