Contacts of the strand formed by residues 70 - 77 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G PHE 3.4 4.7 - - - +
47G VAL* 4.4 11.2 - - + -
64G MET* 3.7 22.7 - - + +
67G ASN* 2.9 35.2 + - + +
68G PRO* 3.1 5.6 - - - +
69G LEU* 1.3 81.4 - - - +
71G SER* 1.3 60.4 + - - +
72G VAL 3.6 21.3 - - - +
73G LEU* 4.3 9.9 - - + -
94G GLY 4.3 0.7 - - - -
95G ALA* 3.1 35.2 + - + +
283G LEU* 3.8 17.9 - - + -
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Residues in contact with SER 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G GLY* 3.5 28.8 + - - -
45G PHE 2.8 22.8 + - - -
46G LYS* 3.9 4.2 - - - +
69G LEU 3.8 1.8 + - - -
70G VAL* 1.3 74.3 - - - +
72G VAL* 1.3 79.3 + - - +
94G GLY 4.4 2.0 - - - +
95G ALA* 3.3 3.4 - - - +
96G VAL* 2.8 29.1 + - - +
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Residues in contact with VAL 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G PHE 3.4 0.8 + - - -
46G LYS* 3.3 35.4 - - + -
47G VAL 2.7 32.4 + - - +
70G VAL* 3.6 5.8 - - - +
71G SER* 1.3 91.4 + - - +
73G LEU* 1.3 58.7 + - - +
74G HIS* 3.7 31.0 - - + +
96G VAL* 3.4 13.9 - - + +
98G ARG* 6.2 1.1 - - + -
113G MET* 4.3 5.8 - - + -
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Residues in contact with LEU 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G VAL* 3.3 18.6 - - + +
49G ILE* 3.9 18.6 - - + -
61G ALA 3.8 21.5 - - - +
64G MET* 3.8 20.6 - - + -
65G LYS* 3.9 19.7 - - + +
70G VAL* 4.3 9.0 - - + -
72G VAL* 1.3 73.2 - - - +
74G HIS* 1.3 63.5 + - - +
75G LEU* 3.8 20.6 - - + -
88G ILE* 4.6 1.3 - - + -
95G ALA* 4.6 5.6 - - + -
96G VAL 2.7 14.5 + - - +
97G VAL* 3.0 42.6 - - + +
98G ARG 3.0 3.3 + - - -
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Residues in contact with HIS 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G LYS* 6.5 0.2 - - + -
47G VAL 2.8 9.2 + - - +
48G ALA* 3.1 9.9 - - + +
49G ILE 2.9 26.3 + - - -
72G VAL* 3.7 25.4 - - + +
73G LEU* 1.3 74.8 - - - +
75G LEU* 1.3 63.5 + - - +
76G TYR* 3.8 1.1 + - - +
98G ARG* 3.6 16.1 - - + +
100G PHE* 3.4 33.5 - + + -
108G ALA 3.7 9.9 - - - -
109G ALA* 2.9 32.3 + - + +
111G THR 4.4 6.3 - - - -
113G MET* 3.6 13.1 - - - -
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Residues in contact with LEU 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ILE* 3.5 23.8 - - + -
52G ALA* 3.5 13.9 - - + -
61G ALA* 3.5 35.2 - - + -
73G LEU* 3.8 12.8 - - + -
74G HIS* 1.3 72.5 - - - +
76G TYR* 1.3 59.8 + - - +
81G ALA* 4.2 5.8 - - + +
84G VAL* 4.2 12.3 - - + -
85G THR* 3.9 20.0 - - - +
88G ILE* 3.7 16.4 - - + -
97G VAL* 3.8 22.7 - - + -
98G ARG 3.0 6.7 + - - -
99G GLY* 3.6 2.1 - - - -
100G PHE* 3.0 26.8 + - - +
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Residues in contact with TYR 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ALA* 6.2 0.2 - - + -
49G ILE 2.9 13.3 + - - +
50G LEU* 4.0 24.2 - - + -
51G GLY 2.6 28.2 + - - -
52G ALA* 2.7 15.4 + - - -
74G HIS 3.8 1.0 + - - +
75G LEU* 1.3 76.3 - - - +
77G ASP* 1.3 87.0 + - - +
78G VAL* 4.0 11.7 - - + +
81G ALA* 4.7 0.7 - - - -
100G PHE* 3.4 19.7 - - + -
101G LEU 4.3 0.4 - - - -
102G GLY* 2.9 39.4 + - - -
103G GLN* 3.4 12.0 + - - -
105G GLN 4.2 1.8 - - - -
106G LEU* 3.8 37.4 - - + +
109G ALA* 4.2 12.6 - - + -
144G LEU* 4.0 16.3 - - + +
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Residues in contact with ASP 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G GLY* 3.0 21.9 - - - +
52G ALA* 5.2 0.2 - - + -
53G ALA* 2.9 36.8 + - + +
54G GLY* 3.6 4.0 + - - -
76G TYR* 1.3 91.2 - - - +
78G VAL* 1.3 85.5 + - - +
79G VAL* 3.4 22.3 + - - +
81G ALA* 4.3 5.6 - - + -
100G PHE 3.3 3.2 + - - -
101G LEU* 3.4 7.3 - - - -
102G GLY 2.9 21.0 + - - -
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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