Contacts of the strand formed by residues 66 - 75 (chain I) in PDB entry 6XAV
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 SER 66 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60I GLN* 4.0 0.9 - - - +
61I SER* 3.0 37.4 + - - +
64I GLY 3.0 5.4 + - - -
65I ASN* 1.3 79.6 - - - +
67I GLU* 1.3 64.0 + - - +
102I LEU* 4.8 0.4 - - - -
103I VAL 4.6 0.2 - - - -
104I ILE* 3.8 20.6 - - - -
105I TYR* 5.1 0.4 - - - -
479I LEU* 2.6 50.5 + - - -
480I SER* 4.2 0.2 - - - -
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Residues in contact with GLU 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I PRO* 3.6 11.7 - - + +
59I ILE 3.4 13.2 - - - +
60I GLN* 3.1 37.4 + - + +
66I SER* 1.3 77.9 - - - +
68I LEU* 1.3 66.9 + - - +
69I GLN* 4.1 16.4 + - - +
101I ARG 3.6 0.5 - - - +
102I LEU* 3.4 8.0 - - - +
103I VAL* 3.2 45.4 + - + +
105I TYR* 2.2 38.2 + - + +
479I LEU* 4.2 2.2 - - - +
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Residues in contact with LEU 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I PHE* 3.6 18.1 - - + -
58I PRO 3.3 0.5 - - - -
59I ILE* 2.6 47.4 + - + +
67I GLU* 1.3 72.6 - - - +
69I GLN* 1.3 56.4 + - - +
100I LEU* 3.7 28.5 - - + -
101I ARG 3.3 34.8 - - - +
102I LEU* 3.9 5.8 - - + +
475I VAL* 3.7 24.5 - - + -
479I LEU* 3.8 16.9 - - + +
489I PRO* 4.3 11.9 - - + -
492I MET* 4.4 9.0 - - - -
493I ILE* 4.6 8.3 - - + -
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Residues in contact with GLN 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I PHE* 3.9 4.3 - - - -
58I PRO* 3.7 21.7 - - + +
67I GLU* 4.1 21.0 + - + +
68I LEU* 1.3 74.5 - - - +
70I TYR* 1.3 63.0 + - - +
71I VAL* 3.8 5.1 + - + +
100I LEU* 3.6 4.3 - - - +
101I ARG* 3.1 79.6 + - + +
103I VAL* 5.5 6.5 - - + +
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Residues in contact with TYR 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I GLU* 2.8 41.2 + - - -
53I PHE* 3.5 39.0 - + + -
54I ARG* 4.5 16.6 - - + -
57I PHE* 3.6 32.9 - - + +
58I PRO* 4.7 0.2 - - - +
69I GLN* 1.3 77.3 - - - +
71I VAL* 1.3 70.2 + - - +
72I SER* 3.3 28.2 - - - -
73I TYR* 3.1 17.8 + - + -
98I VAL* 3.6 20.9 - - + -
100I LEU* 4.0 7.4 - - + -
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Residues in contact with VAL 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I GLN* 4.4 4.5 - - - +
70I TYR* 1.3 86.3 - - - +
72I SER* 1.3 75.9 + - - +
99I LYS* 3.0 26.0 + - + +
100I LEU 4.6 0.9 - - - +
101I ARG* 3.5 54.5 - - + +
119I GLU* 4.5 9.4 - - + +
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Residues in contact with SER 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I GLN* 6.2 0.2 - - - -
50I GLU* 5.9 0.4 - - - -
70I TYR* 3.3 19.0 - - - -
71I VAL* 1.3 93.9 + - - +
73I TYR* 1.3 59.5 + - - +
98I VAL* 3.5 1.4 - - - -
99I LYS* 2.5 50.1 + - - +
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Residues in contact with TYR 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I ILE 4.7 0.2 - - - -
40I GLU 3.2 36.7 + - - -
41I GLN* 3.2 35.6 + - - -
49I LEU* 3.6 33.7 - - + +
50I GLU* 3.2 23.6 - - + -
53I PHE* 4.0 9.4 - + + -
70I TYR* 3.1 25.6 - + + -
72I SER* 1.3 79.4 - - - +
74I ARG* 1.3 68.9 + - - +
75I LEU* 4.3 13.7 - - + -
96I LEU* 4.0 15.3 - - + -
97I ARG 3.2 7.0 - - - -
98I VAL* 3.8 22.2 - - + +
99I LYS* 4.4 1.8 - - - +
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Residues in contact with ARG 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I GLN* 4.9 2.9 - - - +
73I TYR* 1.3 81.9 - - - +
75I LEU* 1.3 78.7 + - - +
76I GLY* 4.4 8.7 - - - -
77I GLU* 6.3 0.6 - - - +
96I LEU* 3.6 2.4 - - - +
97I ARG* 2.5 81.7 + - + +
99I LYS* 5.7 8.0 - - - +
121I GLU* 3.5 25.9 + - - +
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Residues in contact with LEU 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I ILE* 3.7 39.7 - - + +
41I GLN* 5.6 1.9 - - - +
49I LEU* 4.7 0.9 - - + -
73I TYR* 4.3 17.0 - - + -
74I ARG* 1.3 87.7 + - - +
76I GLY* 1.3 68.7 + - - +
77I GLU* 4.9 3.6 - - - +
94I ALA* 5.2 6.3 - - + +
95I PRO 3.4 4.9 - - - +
96I LEU* 3.7 25.1 - - + -
127I ILE* 3.9 23.1 - - + -
129I LEU* 6.1 5.8 - - + -
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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
------------------------------------------------------------
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