Contacts of the strand formed by residues 60 - 70 (chain B) in PDB entry 6FF8
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 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.9 30.4 + - + +
57B THR* 4.1 5.1 - - - +
58B ILE 3.1 7.0 + - - +
59B GLY* 1.3 79.1 - - - +
61B ASP* 1.3 73.1 + - - +
62B PHE* 3.7 26.8 - - + -
80B TRP* 4.0 7.0 - - + -
81B ASP 3.3 13.2 - - - +
82B ILE* 3.9 16.2 - - + -
95B TYR* 3.5 45.8 - - + -
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Residues in contact with ASP 61 (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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62A PHE* 4.1 15.4 - - - +
63A ALA* 5.2 1.9 + - - -
39B THR* 4.6 10.9 - - - +
57B THR* 3.9 12.6 + - + +
60B VAL* 1.3 78.8 - - - +
62B PHE* 1.3 86.0 + - - +
81B ASP* 2.9 54.2 + - + +
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Residues in contact with PHE 62 (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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25A LEU* 5.7 2.2 - - + -
61A ASP* 5.6 0.9 - - - +
62A PHE* 3.1 46.3 - + + +
63A ALA 4.4 8.7 - - - -
64A LEU* 4.3 17.9 - - + -
78A GLN* 2.9 48.2 - - + +
42B ILE* 5.4 1.6 - - - -
60B VAL* 3.7 32.8 - - + -
61B ASP* 1.3 92.3 + - - +
63B ALA* 1.3 65.0 + - - +
79B LEU 3.1 8.5 - - - +
80B TRP* 3.6 41.3 - + + -
81B ASP* 6.0 0.2 - - - -
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Residues in contact with ALA 63 (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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62A PHE* 3.7 11.2 - - - -
42B ILE* 3.5 31.0 - - + -
46B VAL* 4.2 19.1 - - + -
47B HIS* 5.3 7.2 - - + -
62B PHE* 1.3 77.8 - - - +
64B LEU* 1.3 58.9 + - - +
65B LYS 4.2 0.2 - - - -
78B GLN* 3.7 3.1 - - - -
79B LEU* 2.8 35.7 + - + +
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Residues in contact with LEU 64 (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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60A VAL* 5.5 5.6 + - + +
62A PHE* 3.9 14.6 - - + -
80A TRP* 4.9 7.9 - - + -
91A MET* 4.0 15.3 - - + -
94A VAL* 5.2 3.4 - - + -
95A TYR* 3.8 32.3 - - + +
25B LEU* 4.4 9.9 - - + -
46B VAL* 3.5 19.0 - - - +
63B ALA* 1.3 74.6 - - - +
65B LYS* 1.3 64.8 + - - +
66B VAL* 4.1 7.6 + - + +
76B ARG* 4.5 8.1 - - + -
77B LEU 3.2 9.2 - - - +
78B GLN* 3.5 35.9 - - + +
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Residues in contact with LYS 65 (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 TYR* 2.9 72.2 + - + +
46B VAL* 4.0 21.2 + - + +
63B ALA 4.2 0.6 - - - -
64B LEU* 1.3 73.9 - - - +
66B VAL* 1.3 79.0 + - - +
67B LEU* 4.0 11.3 + - + +
76B ARG* 3.3 5.5 - - - +
77B LEU* 2.8 44.2 + - + +
79B LEU* 4.3 6.4 - - + +
182B GLU* 4.5 7.4 + - - -
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Residues in contact with VAL 66 (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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91A MET* 4.0 33.7 - - + -
64B LEU* 4.1 9.4 + - + +
65B LYS* 1.3 88.4 - - - +
67B LEU* 1.3 61.9 + - - +
68B ASN* 4.2 5.0 + - - +
74B LEU* 4.3 26.7 - - + -
75B VAL 3.7 4.7 - - - +
76B ARG* 4.4 9.0 - - + +
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Residues in contact with LEU 67 (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 TYR* 2.9 27.8 - - + +
65B LYS* 3.9 9.8 - - + -
66B VAL* 1.3 75.4 - - - +
68B ASN* 1.3 64.8 + - - +
69B TRP* 3.1 44.2 + - + -
74B LEU* 3.6 4.7 - - - +
75B VAL* 2.7 57.0 + - + +
77B LEU* 4.3 10.5 - - + -
185B ALA* 5.0 2.5 - - + +
186B ARG* 4.4 12.6 - - + +
189B VAL* 4.0 22.0 - - + -
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Residues in contact with ASN 68 (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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66B VAL* 4.2 5.2 + - - +
67B LEU* 1.3 70.5 - - - +
69B TRP* 1.3 67.5 + - - +
70B ASP* 3.4 9.3 + - - +
73B THR 4.1 4.2 + - - -
74B LEU* 3.2 27.3 - - - +
186B ARG* 3.9 8.0 + - - -
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Residues in contact with TRP 69 (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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67B LEU* 3.1 14.7 + - + -
68B ASN* 1.3 74.7 - - - +
70B ASP* 1.3 82.9 + - - +
73B THR* 3.0 30.7 + - + +
75B VAL* 4.0 13.9 - - + -
186B ARG* 3.0 90.0 + - + +
189B VAL* 3.6 22.9 - - + -
190B GLU* 3.7 34.5 - - + -
193B LEU* 3.7 20.8 - - + +
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Residues in contact with ASP 70 (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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68B ASN* 4.4 9.1 + - - +
69B TRP* 1.3 95.3 + - + +
71B SER* 1.3 64.1 + - - +
72B ARG* 2.8 13.2 + - - +
73B THR* 2.7 41.2 + - - +
186B ARG* 5.4 0.4 - - - +
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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