Contacts of the strand formed by residues 135 - 146 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.4 31.4 - - + +
52A THR* 4.2 2.5 - - - +
53A ILE* 3.9 23.8 - - + -
56A ALA* 4.8 1.3 - - + -
87A VAL* 4.1 7.6 - - + +
120A VAL* 3.6 34.5 - - + -
121A ARG 3.6 11.7 - - - +
122A LYS* 4.1 9.0 - - - +
123A VAL* 3.6 7.6 - - - -
127A ILE* 3.5 7.8 - - - +
132A GLN* 3.2 23.4 + - + +
133A GLN 3.3 0.6 - - - -
134A ASP* 1.3 83.9 - - + +
136A GLU* 1.3 60.4 + - - +
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 4.6 4.0 - - - -
88A GLN* 3.3 36.7 + - + +
90A LEU* 3.6 31.1 - - - +
120A VAL* 3.7 3.6 - - - -
121A ARG* 3.0 47.2 + - + +
123A VAL* 3.5 15.1 - - + +
127A ILE* 4.2 6.7 - - + +
135A VAL* 1.3 75.0 - - - +
137A LEU* 1.3 61.8 + - - +
138A HIS* 4.0 9.9 + - + +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 5.0 4.7 - - + -
60A VAL* 4.1 16.8 - - + -
62A VAL* 4.4 16.4 - - + -
80A LEU* 3.8 18.4 - - + -
87A VAL* 4.9 13.7 - - + -
88A GLN 2.9 14.5 + - - +
89A ALA* 3.3 6.1 - - + +
90A LEU 2.9 30.4 + - - -
116A VAL* 3.7 28.0 - - + -
118A GLY* 3.7 33.9 - - - +
119A VAL 3.7 8.5 - - - +
120A VAL* 4.1 6.3 - - + +
136A GLU* 1.3 73.8 - - - +
138A HIS* 1.3 56.5 + - - +
139A VAL* 3.4 1.8 + - - +
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Residues in contact with HIS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 3.8 17.9 - - + +
92A ALA* 4.2 24.5 + - + +
96A HIS* 3.0 42.0 + + - +
118A GLY* 3.2 2.2 - - - -
119A VAL* 2.8 46.6 + - + +
121A ARG* 3.2 43.2 + - + +
136A GLU* 4.0 10.3 + - - +
137A LEU* 1.3 66.8 - - - +
139A VAL* 1.3 71.0 + - - +
140A GLN* 4.1 3.5 - - + +
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA* 4.1 12.6 - - + -
90A LEU 2.9 30.1 + - - +
91A VAL* 3.8 23.1 - - + -
92A ALA 5.4 1.0 + - - +
96A HIS* 4.0 8.5 - - - +
97A ALA* 5.3 4.4 - - - +
101A MET* 4.5 5.4 - - + -
116A VAL* 4.2 11.2 - - + -
118A GLY* 4.1 6.3 - - - -
137A LEU 3.9 8.7 - - - +
138A HIS* 1.3 83.9 - - - +
140A GLN* 1.3 65.1 + - - +
141A LYS 3.4 11.9 - - - +
142A ILE* 3.2 37.5 - - + -
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Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 3.5 36.7 + - - +
59A VAL* 3.9 21.5 - - - +
96A HIS* 4.7 24.7 - - + +
97A ALA* 6.1 0.4 - - - -
101A MET* 3.5 11.0 - - - +
117A GLU* 2.8 29.0 + - - +
118A GLY* 4.4 1.1 - - - +
119A VAL* 3.2 30.5 - - + +
138A HIS* 4.1 7.2 - - + +
139A VAL* 1.3 76.7 - - - +
141A LYS* 1.3 66.3 + - + +
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU 5.9 0.4 - - - -
28A ARG* 3.3 34.5 - - + +
61A TRP* 4.2 14.6 - - + -
101A MET* 3.6 3.6 - - - -
115A ASP 4.5 0.2 - - - -
116A VAL* 3.5 2.3 - - - -
117A GLU* 3.0 55.8 + - + +
139A VAL* 3.4 4.9 - - - +
140A GLN* 1.3 80.4 - - + +
142A ILE* 1.3 72.8 + - - +
143A TYR* 3.7 31.3 + - + +
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Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG 3.2 5.3 + - - -
29A TYR* 3.1 26.3 - - + +
30A GLY 3.6 2.3 + - - +
78A LEU* 4.6 11.7 - - + -
91A VAL* 3.3 25.4 - - + -
101A MET* 3.7 9.4 - - + +
104A PHE* 4.2 5.5 - - + -
105A ALA* 4.4 10.8 - - + -
108A ILE* 3.5 30.1 - - + -
114A VAL* 4.3 15.5 - - + -
115A ASP 3.5 5.2 - - - -
116A VAL* 4.1 13.2 - - + -
139A VAL* 3.2 26.9 - - + -
141A LYS* 1.3 77.5 - - - +
143A TYR* 1.3 62.9 + - - +
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU 2.8 27.2 + - - -
28A ARG 3.3 16.1 + - - -
29A TYR 4.6 8.3 - - - -
30A GLY* 3.4 12.3 - - - +
32A SER* 4.1 28.0 - - - +
43A ARG* 5.9 2.0 - - - -
61A TRP* 4.4 13.9 - + - -
114A VAL* 3.1 5.3 - - - -
115A ASP* 2.8 50.3 + - + +
141A LYS* 3.7 35.5 + - + +
142A ILE* 1.3 76.5 - - - +
144A VAL* 1.3 60.6 + - - +
145A ILE* 3.4 3.8 + - + +
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Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 3.2 6.6 + - - +
31A ILE* 3.6 25.1 - - + +
32A SER* 3.3 22.1 + - - +
104A PHE* 3.9 13.2 - - + -
108A ILE* 3.6 40.6 - - + -
112A SER* 4.2 4.3 - - - -
113A ILE 3.6 6.7 - - - +
114A VAL* 3.8 6.7 - - + -
142A ILE 4.3 0.2 - - - -
143A TYR* 1.3 66.6 - - - +
145A ILE* 1.3 59.7 + - - +
146A SER 3.5 9.0 - - - +
147A LEU* 3.5 37.2 - - + +
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A SER* 3.6 23.8 - - - +
33A SER 5.3 0.2 - - - +
34A MET* 5.1 6.6 - - - -
35A ILE* 3.9 26.1 - - + +
63A ARG* 4.3 4.5 - - - +
113A ILE* 3.2 34.3 + - + +
115A ASP* 3.4 42.0 - - + +
143A TYR* 3.4 6.9 + - + +
144A VAL* 1.3 73.8 - - - +
146A SER* 1.3 68.8 - - - +
147A LEU 4.2 0.2 - - - -
297B TYR* 5.6 0.2 - - + -
433B HIS* 4.8 10.0 + - - +
463B ALA 4.9 0.2 - - - +
465B PRO* 3.9 26.7 - - + -
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A SER* 3.3 7.8 - - - -
113A ILE* 2.9 33.5 + - - +
144A VAL* 3.5 3.1 - - - +
145A ILE* 1.3 89.9 - - - +
147A LEU* 1.3 60.1 + - - +
148A ALA 3.5 0.2 + - - -
433B HIS* 5.0 3.3 + - - -
459B PHE 5.0 1.0 + - - -
462B GLY* 3.5 3.1 + - - -
463B ALA* 2.8 49.0 + - - +
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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