Contacts of the strand formed by residues 74 - 80 (chain B) in PDB entry 3SDI
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 ILE 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B LEU* 2.9 47.7 + - + -
71B ASN* 3.2 22.5 + - - +
73B LYS* 1.3 88.6 - - + +
75B ALA* 1.3 65.0 + - - +
107B ILE* 3.8 22.4 - - + +
109B VAL* 3.9 36.8 - - + -
112B LEU* 3.9 22.7 - - + -
138B TYR* 5.1 4.7 - - + -
139B ALA 3.3 11.9 - - - +
140B GLY* 4.3 0.4 - - - -
141B TYR 5.5 0.2 - - - +
221B GLN* 3.0 14.7 + - - +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.3 16.2 - - + -
67B LEU* 6.4 0.4 - - + -
68B TYR 3.3 15.7 - - - +
69B LYS* 4.5 0.4 - - - -
70B LEU* 4.2 2.0 - - - +
74B ILE* 1.3 77.0 - - - +
76B VAL* 1.3 70.5 + - - +
138B TYR* 3.4 0.7 - - - -
139B ALA 2.8 33.2 + - - +
213B ALA* 6.1 3.8 - - + -
215B ILE* 4.5 7.0 - - + -
221B GLN* 4.0 16.1 - - - +
223B ILE* 6.3 2.7 - - + -
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 4.1 5.8 - - - +
66B LYS 3.5 1.0 - - - +
67B LEU* 3.4 4.7 - - - +
68B TYR* 3.0 52.1 + - + +
70B LEU* 3.8 16.2 - - + -
75B ALA* 1.3 79.2 - - - +
77B ALA* 1.3 59.6 + - - +
78B VAL* 4.4 2.2 - - + -
89B ILE* 4.1 11.9 - - + -
116B LEU* 5.8 0.4 - - + -
136B PHE* 4.0 29.2 - - + -
137B ILE 3.1 8.5 - - - +
138B TYR* 3.2 39.7 - - + -
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 4.0 22.0 - - + -
38B ILE 5.5 0.4 - - - +
48B LEU* 4.0 13.4 - - + +
49B ALA 5.3 1.3 - - - +
50B ALA* 5.2 0.9 - - + -
66B LYS 3.1 5.2 - - - +
67B LEU* 3.6 19.5 - - + -
76B VAL* 1.3 73.8 - - - +
78B VAL* 1.3 62.6 + - - +
135B SER 3.8 0.3 - - - +
136B PHE* 3.5 7.1 - - - -
137B ILE* 2.9 43.1 + - + +
165B VAL* 5.0 0.7 - - - +
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 4.5 3.4 - - - +
65B GLU 4.4 6.1 - - - +
66B LYS* 2.7 53.1 + - + +
68B TYR* 3.8 23.8 - - + -
76B VAL* 4.4 2.7 - - + -
77B ALA* 1.3 77.1 - - - +
79B ALA* 1.3 70.5 + - - +
80B GLY 4.3 5.4 - - - +
81B LEU 4.7 3.6 - - - +
82B THR* 5.1 3.6 - - - -
85B ALA* 3.5 26.0 - - + -
89B ILE* 4.3 1.6 - - + -
134B VAL* 4.7 2.9 - - + -
135B SER 3.8 3.8 - - - +
136B PHE* 3.6 25.4 - - + -
165B VAL* 5.1 0.2 - - - -
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ILE* 3.7 11.7 - - + +
34B ALA* 4.1 3.8 - - + -
35B GLY 4.2 8.1 - - - +
37B ALA* 5.2 0.2 - - + -
66B LYS* 3.9 4.3 - - - +
78B VAL* 1.3 78.1 - - - +
80B GLY* 1.3 57.5 + - - +
134B VAL* 3.7 1.2 - - - -
135B SER 3.0 35.8 + - - +
165B VAL* 3.6 27.6 - - + -
166B GLY* 3.9 22.0 - - - +
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B SER* 5.6 2.2 - - - -
31B ILE* 4.5 7.0 - - - -
34B ALA* 3.7 19.5 - - - +
66B LYS* 4.8 2.3 + - - +
78B VAL* 4.2 4.8 - - - +
79B ALA* 1.3 75.7 - - - +
81B LEU* 1.3 67.3 + - - -
82B THR* 3.3 7.6 + - - -
133B GLY 3.3 9.2 - - - -
134B VAL* 4.6 1.1 - - - -
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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