Contacts of the strand formed by residues 70 - 77 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H GLY* 4.9 0.2 - - - -
45H PHE 3.4 4.0 - - - +
47H VAL* 4.2 10.3 - - + -
64H MET* 3.9 21.3 - - + +
67H ASN* 3.0 28.2 + - + +
68H PRO 3.0 5.6 - - - +
69H LEU* 1.3 79.1 - - - +
71H SER* 1.3 61.6 + - - +
72H VAL 3.6 20.0 - - - +
73H LEU* 4.3 8.5 - - + -
94H GLY* 4.8 0.7 - - - -
95H ALA* 2.9 39.7 + - + +
283H LEU* 3.4 27.8 - - + -
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Residues in contact with SER 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H GLY* 3.7 23.9 + - - -
45H PHE 2.9 19.4 + - - +
46H LYS* 4.1 5.7 - - - +
70H VAL* 1.3 72.6 - - - +
72H VAL* 1.3 73.7 + - - +
94H GLY 5.2 0.4 - - - -
95H ALA* 2.9 5.3 - - - +
96H VAL* 2.5 38.6 + - - +
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Residues in contact with VAL 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H PHE 3.5 1.2 + - - -
46H LYS* 3.4 30.0 - - + -
47H VAL 2.7 32.1 + - - -
70H VAL* 3.6 6.4 - - - +
71H SER* 1.3 90.8 + - - +
73H LEU* 1.3 60.8 + - - +
74H HIS* 3.5 34.5 - - + +
96H VAL* 3.5 12.1 - - + +
98H ARG* 6.0 0.7 - - + -
113H MET* 4.2 8.7 - - + -
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Residues in contact with LEU 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H VAL* 3.3 20.9 - - + +
49H ILE* 4.2 18.6 - - + -
61H ALA 3.6 24.0 - - - +
64H MET* 3.8 18.4 - - + -
65H LYS* 3.6 24.9 - - + +
70H VAL* 4.3 9.2 - - + -
71H SER 4.2 0.2 - - - -
72H VAL* 1.3 72.9 - - - +
74H HIS* 1.3 62.0 + - - +
75H LEU* 4.0 16.6 - - + -
88H ILE* 4.7 1.8 - - + -
95H ALA* 4.4 4.9 - - + -
96H VAL 2.8 12.5 + - - +
97H VAL* 3.1 20.3 - - + +
98H ARG 3.0 23.9 + - - -
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Residues in contact with HIS 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H VAL 2.8 13.1 + - - +
48H ALA* 3.2 7.0 - - + +
49H ILE 2.8 27.9 + - - +
72H VAL* 3.5 20.6 - - + +
73H LEU* 1.3 73.4 - - - +
75H LEU* 1.3 64.7 + - - +
76H TYR* 3.9 0.7 + - - +
98H ARG* 3.3 19.7 - - + +
100H PHE* 3.3 35.0 - + + -
108H ALA 3.9 7.4 - - - -
109H ALA* 2.8 31.0 + - + +
111H THR 4.7 1.8 - - - -
113H MET* 3.2 22.9 - - + +
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Residues in contact with LEU 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H ILE* 3.8 11.9 - - + -
52H ALA* 3.5 16.2 - - + -
61H ALA* 3.6 22.7 - - + -
73H LEU* 4.0 15.7 - - + -
74H HIS* 1.3 77.3 - - - +
76H TYR* 1.3 56.0 + - - +
81H ALA* 3.9 6.3 - - + +
84H VAL* 4.1 11.2 - - + -
85H THR* 3.7 28.5 - - - +
88H ILE* 4.0 22.0 - - + -
97H VAL* 3.9 21.3 - - + -
98H ARG 2.9 8.7 + - - -
99H GLY* 3.3 1.0 - - - -
100H PHE* 2.7 33.7 + - - +
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Residues in contact with TYR 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H ILE 3.0 6.9 + - - -
50H LEU* 3.5 36.6 - - + -
51H GLY 2.6 30.6 + - - -
52H ALA* 3.0 4.7 + - - -
74H HIS 3.9 1.2 + - - +
75H LEU* 1.3 73.9 - - - +
77H ASP* 1.3 82.7 + - - +
78H VAL* 3.9 16.0 - - + +
81H ALA* 4.5 0.7 - - - -
100H PHE* 3.3 19.5 - - + -
102H GLY 3.0 38.3 - - - -
103H GLN* 3.5 16.2 + - - +
105H GLN 4.4 3.6 - - - -
106H LEU* 3.8 27.1 - - + -
109H ALA* 4.1 12.6 - - + -
144H LEU* 4.1 13.8 - - + +
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Residues in contact with ASP 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H GLY* 3.1 20.8 - - - +
53H ALA* 2.8 39.2 + - + +
54H GLY* 3.6 3.3 + - - -
76H TYR* 1.3 89.3 - - - +
78H VAL* 1.3 84.2 + - - +
79H VAL* 3.1 24.6 + - - +
81H ALA* 4.0 4.4 - - + +
100H PHE 3.3 2.7 + - - +
101H LEU* 3.3 9.2 - - - +
102H GLY 3.1 18.0 + - - -
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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