Contacts of the strand formed by residues 70 - 77 (chain B) in PDB entry 1SMK
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 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLY* 4.9 0.2 - - - -
45B PHE 3.4 5.4 - - - +
47B VAL* 4.0 8.7 - - + -
64B MET* 3.5 42.6 - - + +
67B ASN* 2.9 20.6 + - + +
68B PRO 4.2 5.2 - - - +
69B LEU* 1.3 76.6 - - - +
71B SER* 1.3 58.5 + - - +
72B VAL 3.3 26.5 - - - +
73B LEU* 4.1 9.0 - - + -
94B GLY* 4.2 0.7 - - - -
95B ALA* 3.1 37.9 + - + +
283B LEU* 3.8 13.7 - - + -
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Residues in contact with SER 71 (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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44B GLY* 3.4 29.2 + - - -
45B PHE 2.8 15.8 + - - -
46B LYS* 4.0 6.2 - - - +
69B LEU 3.5 2.4 + - - -
70B VAL* 1.3 73.9 - - - +
72B VAL* 1.3 79.8 + - - +
94B GLY 4.0 3.5 - - - +
95B ALA* 3.2 3.6 - - - +
96B VAL* 2.8 27.2 + - - +
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Residues in contact with VAL 72 (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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45B PHE 3.4 0.8 + - - -
46B LYS* 3.5 26.0 - - + -
47B VAL 2.8 26.3 + - - -
70B VAL* 3.3 8.4 - - - +
71B SER* 1.3 93.9 + - - +
73B LEU* 1.3 64.1 + - - +
74B HIS* 3.3 33.9 - - + +
96B VAL* 3.5 14.6 - - + +
98B ARG* 5.9 2.5 - - + -
113B MET* 4.5 7.6 - - + -
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Residues in contact with LEU 73 (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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47B VAL* 3.1 21.3 - - + +
49B ILE* 3.9 26.7 - - + -
61B ALA 3.7 23.3 - - - +
64B MET* 4.0 10.8 - - + -
65B LYS* 3.9 21.1 - - + +
70B VAL* 4.1 9.0 - - + -
72B VAL* 1.3 74.3 - - - +
74B HIS* 1.3 63.9 + - - +
75B LEU* 4.0 17.7 - - + -
88B ILE* 4.6 2.2 - - + -
95B ALA* 4.4 4.0 - - + -
96B VAL 2.8 14.5 + - - +
97B VAL* 3.2 18.5 - - + +
98B ARG 3.0 24.9 + - - -
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Residues in contact with HIS 74 (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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47B VAL 2.7 9.5 + - - +
48B ALA* 3.2 11.1 - - + +
49B ILE* 2.8 32.9 + - - +
72B VAL* 3.3 28.5 - - + +
73B LEU* 1.3 77.7 - - - +
75B LEU* 1.3 61.0 + - - +
76B TYR* 3.8 0.8 + - - -
98B ARG* 3.5 21.4 - - + +
100B PHE* 3.3 36.5 - + + -
108B ALA 3.7 9.0 - - - -
109B ALA* 2.7 29.4 + - + +
111B THR 4.6 1.8 - - - -
113B MET* 3.5 20.8 - - + +
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Residues in contact with LEU 75 (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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49B ILE* 4.0 13.9 - - + -
52B ALA* 3.6 17.0 - - + -
61B ALA* 3.5 22.2 - - + -
73B LEU* 4.0 9.0 - - + -
74B HIS* 1.3 77.4 - - - +
76B TYR* 1.3 60.5 + - - +
81B ALA* 3.9 7.6 - - + +
84B VAL* 4.0 10.8 - - + -
85B THR* 3.6 31.0 - - - +
88B ILE* 3.7 24.5 - - + -
97B VAL* 3.8 21.5 - - + -
98B ARG 3.0 8.3 + - - -
99B GLY* 3.4 1.7 - - - -
100B PHE* 2.9 27.3 + - - +
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Residues in contact with TYR 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 ALA* 6.2 0.2 - - + -
49B ILE 3.0 14.3 + - - +
50B LEU* 4.0 22.9 - - + -
51B GLY 2.8 22.8 + - - -
52B ALA* 2.9 7.2 + - - -
74B HIS 3.8 1.3 + - - +
75B LEU* 1.3 74.5 - - - +
77B ASP* 1.3 93.7 + - - +
78B VAL* 3.9 13.2 - - + +
81B ALA* 4.5 0.9 - - - -
100B PHE* 3.4 17.7 - - + -
102B GLY* 3.1 41.5 - - - -
103B GLN* 3.2 9.7 + - - -
105B GLN 4.2 0.2 - - - -
106B LEU* 3.6 44.9 - - + +
109B ALA* 4.1 11.9 - - + -
144B LEU* 4.2 14.0 - - + +
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Residues in contact with ASP 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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51B GLY* 3.0 21.2 - - - +
53B ALA* 2.8 39.1 + - + +
54B GLY 3.8 2.9 + - - -
76B TYR* 1.3 90.5 - - - +
78B VAL* 1.3 83.6 + - - +
79B VAL* 3.3 21.5 + - - +
81B ALA* 4.1 6.0 - - + +
100B PHE 3.3 9.4 + - - +
101B LEU* 3.4 3.3 - - - +
102B GLY 3.1 19.1 + - - -
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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