Contacts of the strand formed by residues 97 - 104 (chain A) in PDB entry 3F40
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 GLU 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.3 1.7 - - - +
28A LYS 5.3 4.6 - - - +
29A ARG 3.7 8.5 - - - +
30A LEU 4.2 5.3 - - - +
31A ASN* 2.7 54.0 + - + +
32A GLU 5.0 1.0 + - - -
93A LEU* 3.2 8.5 - - - +
94A GLU 3.0 32.7 + - - +
95A LYS* 3.8 12.5 - - - +
96A GLY* 1.3 84.3 - - - +
98A ILE* 1.3 64.0 + - - +
99A THR* 3.5 1.1 + - - +
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Residues in contact with ILE 98 (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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10A LEU* 4.4 8.3 - - + +
11A VAL* 4.5 7.9 - - + -
14A PHE* 3.8 38.8 - - + -
29A ARG* 2.9 23.8 + - + +
30A LEU* 3.6 10.1 - - + -
31A ASN* 2.9 21.7 + - - +
34A PHE* 3.7 20.3 - - + -
91A TYR* 4.2 20.4 - - + -
92A HIS 3.5 7.2 - - - +
93A LEU* 3.7 21.1 - - + -
97A GLU* 1.3 71.7 - - - +
99A THR* 1.3 61.3 + - - +
100A SER 3.7 19.5 - - - +
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Residues in contact with THR 99 (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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31A ASN* 4.0 24.9 - - + +
33A ASN 4.3 1.7 - - - +
34A PHE* 3.3 7.5 - - - -
35A THR* 3.1 21.0 + - - +
92A HIS* 2.8 35.3 + - - +
94A GLU* 3.9 31.8 - - + +
97A GLU* 4.0 6.5 - - - +
98A ILE* 1.3 76.0 - - - +
100A SER* 1.3 63.8 + - - +
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Residues in contact with SER 100 (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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34A PHE* 3.7 5.8 - - - -
35A THR* 3.2 23.6 - - - -
90A LEU 4.3 0.4 + - - -
91A TYR* 3.4 4.5 - - - -
92A HIS* 3.0 46.2 + - - +
98A ILE* 3.6 5.7 - - - +
99A THR* 1.3 83.1 + - - +
101A LEU* 1.3 61.5 + - - +
102A HIS* 4.2 19.2 + - - -
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Residues in contact with LEU 101 (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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14A PHE* 5.4 3.8 - - + -
34A PHE* 3.8 15.5 - - + -
35A THR 3.0 5.7 + - - +
36A PHE* 3.4 17.4 - - + -
37A ASN 2.9 25.3 + - - -
49A TYR* 3.7 27.8 - - + +
60A TYR* 6.5 0.4 - - + -
76A TYR* 4.1 4.5 - - - +
89A GLY* 4.0 4.7 - - - -
90A LEU 3.3 13.7 - - - +
91A TYR* 3.5 47.1 - - + +
100A SER* 1.3 75.7 - - - +
102A HIS* 1.3 82.0 + - - +
103A VAL* 4.1 3.8 - - + +
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Residues in contact with HIS 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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35A THR* 5.1 2.0 - - - -
37A ASN* 3.3 37.7 + - + +
90A LEU* 2.8 47.8 + - + +
100A SER* 4.2 22.8 + - - -
101A LEU* 1.3 76.5 - - - +
103A VAL* 1.3 61.2 + - - +
104A TYR* 3.7 25.7 - + + +
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Residues in contact with VAL 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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36A PHE* 3.6 34.5 - - + -
37A ASN 2.9 7.9 + - - +
38A GLY* 3.7 10.2 - - - -
39A PRO* 3.4 14.6 - - - +
76A TYR* 4.0 16.8 - - - +
78A ILE* 4.2 7.4 - - + -
87A ALA* 4.0 10.8 - - + -
88A SER 3.5 10.5 - - - +
101A LEU* 4.1 9.1 - - + -
102A HIS* 1.3 74.6 - - - +
104A TYR* 1.3 64.4 - - - +
105A PHE* 3.9 28.3 - - + -
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Residues in contact with TYR 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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39A PRO* 5.1 0.4 - - - -
87A ALA* 3.3 2.1 - - - -
88A SER* 2.8 53.9 + - - +
90A LEU* 4.1 24.7 - - + +
102A HIS* 3.7 30.3 - + + +
103A VAL* 1.3 77.7 - - - +
105A PHE* 1.3 65.9 + - - +
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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