Contacts of the strand formed by residues 93 - 104 (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 93 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78I PRO* 3.5 22.0 - - - +
79I VAL* 4.2 5.2 + - - +
91I THR* 3.4 23.8 + - - +
92I TYR* 1.3 75.1 - - - +
94I ALA* 1.3 62.5 + - - +
95I PRO* 4.6 0.3 - - - +
126I GLU* 3.2 31.7 + - - +
127I ILE 3.2 19.1 - - - -
128I PRO* 3.7 9.2 - - - -
129I LEU* 4.0 4.3 - - - -
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Residues in contact with ALA 94 (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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75I LEU* 5.1 6.8 - - + +
76I GLY 3.4 26.9 - - - +
77I GLU 4.2 6.3 - - - -
78I PRO* 4.2 2.0 - - + -
93I SER* 1.3 74.6 - - - +
95I PRO* 1.3 70.8 - - + +
96I LEU 3.7 1.2 + - - -
126I GLU* 3.1 10.6 - - - +
127I ILE* 3.5 18.2 + - - +
129I LEU* 3.4 29.2 - - + +
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Residues in contact with PRO 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I LEU* 3.3 3.7 - - - +
76I GLY* 2.4 41.4 + - - -
77I GLU 3.4 20.6 - - - +
79I VAL* 5.4 8.5 - - + -
93I SER 4.6 0.7 - - - +
94I ALA* 1.3 87.4 - - + +
96I LEU* 1.3 59.7 + - - +
97I ARG* 3.5 37.0 - - - +
123I TYR* 4.0 5.6 - - + -
126I GLU* 3.3 21.3 - - - +
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Residues in contact with LEU 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I LEU* 5.3 4.3 - - + -
53I PHE* 4.5 3.8 - - + -
73I TYR* 4.0 14.4 - - + -
74I ARG 3.7 7.0 - - - +
75I LEU* 3.7 26.0 - - + -
94I ALA 3.7 2.0 + - - +
95I PRO* 1.3 73.7 - - - +
97I ARG* 1.3 61.4 + - - +
98I VAL* 3.8 25.3 + - + -
122I VAL 3.6 0.7 - - - +
123I TYR* 3.4 7.4 - - - -
124I MET* 3.2 46.5 + - + +
125I GLY* 4.2 9.4 + - - +
127I ILE* 4.9 16.8 - - + -
464I PHE* 4.3 28.7 - - + -
498I ILE* 5.6 1.3 - - + -
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Residues in contact with ARG 97 (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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73I TYR* 3.2 1.2 - - - -
74I ARG* 2.5 82.9 + - - +
76I GLY* 4.5 7.5 - - - +
95I PRO* 3.5 28.2 - - - +
96I LEU* 1.3 73.4 - - - +
98I VAL* 1.3 59.7 + - - +
99I LYS* 4.2 1.4 + - - +
121I GLU* 3.8 21.7 - - + +
122I VAL 3.5 8.7 - - - +
123I TYR* 3.2 40.6 - - - +
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Residues in contact with VAL 98 (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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53I PHE* 3.9 13.9 - - + -
57I PHE* 6.1 0.7 - - + -
70I TYR* 3.6 30.5 - - + -
72I SER 3.6 4.5 - - - +
73I TYR* 3.8 11.4 - - + -
96I LEU* 3.8 19.5 - - + -
97I ARG* 1.3 76.5 - - - +
99I LYS* 1.3 62.2 + - - +
100I LEU* 3.4 18.8 + - + -
121I GLU* 4.0 0.2 - - - -
122I VAL* 2.8 37.2 + - - +
124I MET* 3.7 31.4 - - + -
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Residues in contact with LYS 99 (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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70I TYR* 4.0 0.3 - - - -
71I VAL* 3.0 37.9 + - + +
72I SER* 2.5 35.3 + - - +
73I TYR* 5.5 1.3 - - - -
74I ARG* 5.8 9.0 - - + +
97I ARG 5.3 2.0 - - - +
98I VAL* 1.3 68.7 - - - +
100I LEU* 1.3 64.9 + - - +
119I GLU* 5.5 8.5 - - + +
120I GLN* 3.4 11.6 - - - +
121I GLU* 3.4 41.9 + - + +
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Residues in contact with LEU 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I PHE* 3.7 28.7 - - + -
68I LEU* 3.7 28.5 - - + -
69I GLN 3.6 8.7 - - - +
70I TYR* 4.0 7.9 - - + -
71I VAL* 4.6 0.4 - - - +
98I VAL* 3.4 23.1 + - + -
99I LYS* 1.3 73.8 - - - +
101I ARG* 1.3 65.8 + - - +
118I LYS 4.0 0.6 - - - +
119I GLU* 3.8 4.2 - - - +
120I GLN* 3.1 37.0 + - - +
122I VAL* 4.2 10.5 - - + -
124I MET* 3.9 11.2 - - + -
489I PRO* 5.1 2.9 - - + +
493I ILE* 3.7 31.9 - - + -
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Residues in contact with ARG 101 (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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67I GLU 3.6 1.9 - - - +
68I LEU* 3.3 6.9 - - - +
69I GLN* 3.1 61.1 + - + +
71I VAL* 3.5 27.9 - - + +
100I LEU* 1.3 80.6 - - - +
102I LEU* 1.3 59.8 + - - +
103I VAL* 4.1 11.4 + - + +
117I ILE* 3.6 35.7 - - + +
118I LYS 3.3 6.7 - - - +
119I GLU* 3.1 39.2 + - + -
489I PRO* 5.3 0.2 - - - -
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Residues in contact with LEU 102 (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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67I GLU 3.4 18.2 - - - +
68I LEU* 3.9 3.7 - - + +
101I ARG* 1.3 73.6 - - - +
103I VAL* 1.3 75.4 + - - +
104I ILE* 4.8 13.7 - - + -
116I ASP 4.3 0.3 - - - +
117I ILE* 4.0 1.2 - - - -
118I LYS* 3.1 40.2 + - + +
479I LEU* 3.7 31.2 - - + -
485I ASP* 6.2 2.9 - - - -
487I LEU* 4.7 12.1 - - + +
489I PRO* 3.9 30.8 - - + +
492I MET* 4.0 22.9 - - + -
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Residues in contact with VAL 103 (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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65I ASN 3.8 2.3 - - - +
67I GLU* 3.2 52.9 + - + +
69I GLN* 5.4 6.7 - - + +
101I ARG* 4.1 20.9 - - + +
102I LEU* 1.3 81.8 - - - +
104I ILE* 1.3 76.0 + - - +
105I TYR* 4.1 10.3 - - + +
114I VAL* 3.8 30.1 - - + -
116I ASP 4.9 0.4 - - - -
117I ILE* 4.1 13.2 - - + -
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Residues in contact with ILE 104 (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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64I GLY 5.1 2.0 - - - +
65I ASN* 3.9 3.6 - - + +
66I SER* 3.8 26.9 - - - +
102I LEU* 4.8 14.8 - - + -
103I VAL* 1.3 82.9 - - - +
105I TYR* 1.3 72.6 + - - +
107I ARG* 4.5 4.5 - - - +
114I VAL* 3.4 8.4 - - + +
115I LYS* 3.2 36.8 + - + +
116I ASP* 4.9 9.3 + - - +
479I LEU* 6.0 0.7 - - + -
483I ASP 4.4 13.0 - - - +
484I LEU* 3.8 27.8 - - + -
485I ASP* 4.7 17.0 - - + +
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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