Contacts of the strand formed by residues 102 - 107 (chain A) in PDB entry 4LAX
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 VAL 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.8 1.4 - - - +
38A LYS* 2.8 52.0 + - + +
39A ARG* 3.0 52.9 + - + +
100A GLY 3.7 0.6 + - - -
101A GLU* 1.3 77.5 - - - +
103A CYS* 1.3 64.7 + - - +
131A GLU* 4.1 16.6 - - + -
132A VAL 3.3 9.2 - - - +
133A GLU* 3.9 20.0 - - + +
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Residues in contact with CYS 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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35A LYS* 3.9 27.4 - - + -
36A VAL 3.3 12.6 - - - +
37A ILE* 4.2 3.4 - - - -
38A LYS 4.1 1.3 - - - +
93A ALA* 5.6 1.1 - - - -
97A MET* 3.7 29.6 - - - -
101A GLU* 4.0 6.5 - - - +
102A VAL* 1.3 75.2 - - - +
104A HIS* 1.3 66.8 + - - +
105A ILE* 4.2 17.7 - - - -
130A PHE 3.7 0.3 - - - +
131A GLU* 3.4 4.9 - - - +
132A VAL* 2.9 39.3 + - - -
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Residues in contact with HIS 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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34A LEU 3.8 0.7 - - - +
35A LYS* 3.4 3.3 - - - +
36A VAL* 2.8 46.8 + - + +
38A LYS* 3.0 32.0 - - + +
60A TRP* 5.1 9.4 - + - -
103A CYS* 1.3 80.8 - - - +
105A ILE* 1.3 61.7 + - - +
106A THR* 5.6 0.4 - - - -
129A VAL* 4.9 13.7 - - + +
130A PHE 3.2 5.6 - - - +
131A GLU* 2.7 41.3 + - + +
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Residues in contact with ILE 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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33A VAL* 4.6 5.4 - - + -
34A LEU 3.2 10.1 - - - +
35A LYS* 4.0 17.7 - - + -
89A ALA* 4.2 4.3 - - + +
90A TRP* 4.1 22.4 - - + +
93A ALA* 3.7 35.2 - - + -
94A ILE* 6.0 0.4 - - + -
103A CYS* 4.2 9.8 - - - -
104A HIS* 1.3 77.6 - - - +
106A THR* 1.3 62.1 + - - +
107A CYS* 3.7 21.8 - - - -
128A LEU 3.7 0.9 - - - +
129A VAL* 3.3 6.8 - - - +
130A PHE* 2.9 51.8 + - + +
132A VAL* 4.8 9.2 - - + -
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Residues in contact with THR 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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32A GLY 3.5 1.9 - - - +
33A VAL* 3.4 6.1 - - - +
34A LEU* 2.8 57.8 + - + +
62A LEU* 4.7 6.1 - - + -
104A HIS 5.6 0.5 - - - -
105A ILE* 1.3 72.3 + - - +
107A CYS* 1.3 62.6 + - - +
108A LYS* 4.1 7.2 - - + +
127A THR* 3.7 23.8 - - + -
128A LEU 3.4 4.9 - - - +
129A VAL* 4.2 16.5 - - + +
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Residues in contact with CYS 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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32A GLY 3.6 4.3 - - - -
33A VAL* 5.1 0.7 - - - -
87A ILE* 5.0 0.2 - - - -
89A ALA* 3.4 33.9 - - + -
105A ILE* 3.7 25.8 - - - -
106A THR* 1.3 76.7 - - - +
108A LYS* 1.3 67.4 + - - +
112A ALA* 4.5 7.6 - - + +
126A ALA 4.2 0.9 - - - +
127A THR* 3.4 5.7 - - - -
128A LEU* 2.8 45.3 + - + +
130A PHE* 3.9 20.9 - - - -
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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