Contacts of the strand formed by residues 135 - 146 (chain H) in PDB entry 6IY6
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 135 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H LEU* 3.4 32.1 - - + +
52H THR* 4.2 2.7 - - - +
53H ILE* 3.9 24.2 - - + -
56H ALA* 4.8 1.8 - - + -
87H VAL* 4.1 7.8 - - + +
88H GLN* 5.0 1.4 + - - +
120H VAL* 3.6 34.3 - - + -
121H ARG 3.6 10.5 - - - +
122H LYS* 4.1 8.3 - - - +
123H VAL* 3.6 8.6 - - - +
127H ILE* 4.6 3.5 - - - +
132H GLN* 3.2 23.7 - - + +
133H GLN 3.3 1.5 + - - +
134H ASP* 1.3 83.3 - - + +
136H GLU* 1.3 62.1 + - - +
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Residues in contact with GLU 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H PHE* 4.1 0.5 - - - -
87H VAL* 4.6 4.0 - - - -
88H GLN* 3.3 39.0 + - + +
90H LEU* 3.5 29.9 - - - +
120H VAL* 3.7 4.3 - - - -
121H ARG* 3.0 37.9 + - + +
122H LYS 5.8 0.6 - - - +
123H VAL* 3.5 16.9 - - + +
127H ILE* 5.5 0.2 - - + -
135H VAL* 1.3 75.2 - - - +
137H LEU* 1.3 60.1 + - - +
138H HIS* 2.9 33.5 + - + -
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Residues in contact with LEU 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H LEU* 4.9 8.1 - - + -
60H VAL* 4.1 16.2 - - + -
62H VAL* 4.4 17.0 - - + -
80H LEU* 3.8 18.4 - - + -
87H VAL* 4.7 9.8 - - + +
88H GLN 2.9 14.4 + - - +
89H ALA* 3.3 6.1 - - + +
90H LEU 2.8 30.4 + - - -
116H VAL* 3.7 27.6 - - + -
118H GLY* 3.6 34.5 - - - +
119H VAL 3.7 8.7 - - - +
120H VAL* 4.1 7.2 - - + +
136H GLU* 1.3 70.1 - - - +
138H HIS* 1.3 58.0 + - - +
139H VAL 3.4 1.8 + - - +
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Residues in contact with HIS 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H LEU* 3.8 22.7 + - + +
92H ALA* 5.4 8.3 - - + +
96H HIS* 5.3 8.7 + - + +
118H GLY* 3.2 2.4 - - - -
119H VAL* 2.8 45.0 + - + +
121H ARG* 3.2 61.3 + - + +
136H GLU* 2.9 33.9 + - + -
137H LEU* 1.3 67.6 - - - +
139H VAL* 1.3 62.7 + - - +
140H GLN* 4.0 2.9 - - - +
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Residues in contact with VAL 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H LEU* 5.1 1.1 - - + -
89H ALA* 4.1 12.6 - - + -
90H LEU 2.9 29.3 + - - +
91H VAL* 3.8 31.3 - - + -
92H ALA 5.5 1.6 + - - -
96H HIS* 4.0 15.6 - - - +
97H ALA* 5.2 4.0 - - - +
101H MET* 4.5 6.7 - - + -
116H VAL* 4.2 13.7 - - + -
117H GLU 4.9 0.2 - - - -
118H GLY* 4.1 6.3 - - - -
137H LEU 3.9 8.5 - - - +
138H HIS* 1.3 72.5 - - - +
140H GLN* 1.3 65.2 + - - +
141H LYS 3.4 26.7 - - - +
142H ILE* 4.4 10.5 - - + -
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Residues in contact with GLN 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ARG* 3.5 35.3 + - - +
59H VAL* 3.9 21.5 - - - +
96H HIS* 4.7 21.7 + - + +
97H ALA* 6.1 0.4 - - - -
101H MET* 3.5 11.4 - - - +
117H GLU* 2.8 28.2 + - - +
118H GLY 4.4 0.7 - - - +
119H VAL* 3.2 30.4 - - + +
121H ARG* 5.9 1.0 - - - +
138H HIS 4.0 6.7 - - - +
139H VAL* 1.3 77.5 - - - +
141H LYS* 1.3 65.9 + - + +
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Residues in contact with LYS 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H GLU 6.0 0.4 - - - -
28H ARG* 3.3 33.0 - - + +
61H TRP* 4.2 18.9 - - + -
101H MET* 3.6 2.2 - - - -
115H ASP 4.5 0.7 - - - -
116H VAL* 3.5 4.6 - - - -
117H GLU* 3.0 55.1 + - + +
139H VAL* 3.4 14.5 - - - +
140H GLN* 1.3 80.4 - - + +
142H ILE* 1.3 59.4 + - - +
143H TYR* 3.7 27.1 + - + +
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Residues in contact with ILE 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ARG 3.2 5.1 + - - -
29H TYR* 3.2 27.6 - - + +
30H GLY 3.6 2.6 + - - +
78H LEU* 3.9 24.9 - - + -
80H LEU* 5.6 0.7 - - + -
91H VAL* 5.0 4.5 - - + -
101H MET* 3.7 19.9 - - + +
104H PHE* 4.2 12.3 - - + -
105H ALA* 4.8 12.6 - - + -
108H ILE* 3.6 28.7 - - + -
114H VAL* 4.2 11.9 - - + -
115H ASP 3.5 4.5 - - - -
116H VAL* 4.1 20.4 - - + -
139H VAL* 4.4 9.2 - - + -
141H LYS* 1.3 74.5 - - - +
143H TYR* 1.3 61.8 + - - +
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Residues in contact with TYR 143 (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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27H GLU 2.8 25.2 + - - -
28H ARG* 3.3 21.0 + - - -
29H TYR* 3.7 18.4 - - - -
30H GLY 3.4 8.7 - - - +
32H SER* 4.1 22.2 - - - +
43H ARG* 4.9 7.4 - - - -
61H TRP* 4.1 32.3 - + - -
114H VAL* 3.1 5.3 - - - -
115H ASP* 2.8 43.9 + - + +
141H LYS* 3.7 24.3 + - + +
142H ILE* 1.3 72.6 - - - +
144H VAL* 1.3 60.6 + - - +
145H ILE* 3.4 4.1 + - + +
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Residues in contact with VAL 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H GLY 3.2 8.2 + - - +
31H ILE* 3.7 15.3 - - + +
32H SER* 3.3 22.1 + - - +
104H PHE* 3.9 13.7 - - + -
108H ILE* 3.6 40.8 - - + -
112H SER* 4.2 4.0 - - - -
113H ILE 3.6 7.0 - - - +
114H VAL* 3.8 6.7 - - + -
142H ILE 4.4 0.2 + - - -
143H TYR* 1.3 66.8 - - - +
145H ILE* 1.3 59.3 + - - +
146H SER 3.5 22.7 - - - +
147H LEU* 3.5 32.0 + - + +
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Residues in contact with ILE 145 (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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297G TYR* 5.5 0.9 - - + -
433G HIS* 5.0 9.5 + - - +
465G PRO* 4.0 25.4 - - + -
32H SER* 3.6 24.5 - - - +
33H SER 5.2 0.4 - - - +
34H MET* 5.0 8.8 - - - -
35H ILE* 3.9 26.1 - - + +
63H ARG* 4.0 4.9 - - - -
113H ILE* 3.1 33.6 + - + +
115H ASP* 3.4 40.8 - - + +
143H TYR* 3.4 6.9 + - + +
144H VAL* 1.3 72.2 - - - +
146H SER* 1.3 70.4 + - - +
147H LEU 4.2 0.2 - - - -
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Residues in contact with SER 146 (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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433G HIS* 5.0 3.8 - - - -
459G PHE 5.2 0.9 + - - -
462G GLY* 3.6 3.5 + - - -
463G ALA* 3.0 42.9 + - - +
112H SER* 3.3 6.8 - - - -
113H ILE* 2.9 36.9 + - - +
144H VAL* 3.5 3.3 - - - +
145H ILE* 1.3 92.3 - - - +
147H LEU* 1.3 59.9 + - - +
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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