Contacts of the strand formed by residues 110 - 121 (chain A) in PDB entry 6U6V
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 GLY 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ARG* 4.2 8.7 - - - -
108A ASP 3.7 1.2 + - - -
109A SER* 1.3 77.7 - - - +
111A LEU* 1.3 60.6 + - - -
112A TYR* 3.6 6.9 - - - -
133A GLU* 3.5 6.5 - - - +
134A LEU 2.8 34.5 + - - +
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Residues in contact with LEU 111 (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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42A ARG* 3.0 8.1 - - - +
43A SER 2.9 41.2 + - - +
44A SER* 3.2 41.5 - - - +
45A ARG* 3.4 29.8 - - + +
50A THR* 3.8 15.0 - - + -
110A GLY* 1.3 71.7 - - - -
112A TYR* 1.3 64.9 + - - +
113A CYS* 4.3 7.6 - - - -
131A ALA* 4.3 1.8 - - + -
132A MET 3.6 24.7 - - - +
133A GLU* 4.1 9.6 - - + +
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Residues in contact with TYR 112 (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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20A LEU* 3.6 22.7 - - + -
40A TRP* 4.5 9.4 - + + -
41A TYR 3.7 2.5 - - - -
42A ARG* 3.5 25.2 + - + -
57A ILE* 3.6 37.0 - - + +
99A ILE* 5.1 1.6 - - + -
101A MET* 3.5 35.9 - - - +
108A ASP* 2.5 33.4 + - - -
110A GLY 3.6 13.2 - - - -
111A LEU* 1.3 76.4 - - - +
113A CYS* 1.3 61.5 + - - +
130A GLY 3.8 0.3 - - - +
131A ALA* 3.4 2.8 - - - +
132A MET* 2.7 46.6 + - + +
134A LEU* 3.9 19.5 - - + -
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Residues in contact with CYS 113 (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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39A THR 3.9 0.2 - - - +
40A TRP* 3.2 12.0 - - - -
41A TYR* 2.8 49.6 + - + +
43A SER* 3.6 17.3 - - - -
51A CYS* 2.0 59.2 - - + -
111A LEU* 4.3 8.3 - - - -
112A TYR* 1.3 78.8 - - - +
114A CYS* 1.3 60.3 + - - +
115A LEU 3.9 0.7 + - - -
130A GLY 3.1 4.5 - - - +
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Residues in contact with CYS 114 (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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3A VAL* 3.8 7.2 - - - -
22A CYS* 2.0 51.1 - - + -
39A THR 3.5 4.7 - - - -
40A TRP* 3.7 21.5 - - + -
97A PHE* 3.8 13.5 - - + -
113A CYS* 1.3 73.1 - - - +
115A LEU* 1.3 61.7 + - - +
116A VAL* 4.2 1.2 + - - +
129A HIS* 3.1 8.2 - - - +
130A GLY* 2.9 36.0 + - - -
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Residues in contact with LEU 115 (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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37A TYR* 4.4 3.8 - - + -
38A LYS* 3.2 4.9 - - - -
39A THR* 2.8 41.8 + - + +
41A TYR* 3.7 24.9 - - + +
54A ARG* 3.1 43.1 - - - +
97A PHE* 3.8 0.9 - - - -
113A CYS 3.9 1.4 + - - -
114A CYS* 1.3 75.0 - - - +
116A VAL* 1.3 67.4 + - - +
117A VAL* 4.2 17.3 - - + -
127A ARG* 4.4 13.9 - - + -
128A VAL 3.3 24.2 - - - +
129A HIS* 4.2 8.7 - - + -
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Residues in contact with VAL 116 (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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1A PHE* 4.1 18.8 - - + -
3A VAL* 4.1 12.8 - - + -
22A CYS* 5.8 0.4 - - + -
24A LEU* 3.7 34.8 - - + -
36A PHE* 4.3 7.6 - - + -
37A TYR 3.4 3.4 - - - -
38A LYS* 4.0 24.0 - - + -
97A PHE* 4.1 20.6 - - + -
114A CYS* 4.9 3.1 - - + -
115A LEU* 1.3 80.0 - - - +
117A VAL* 1.3 62.3 + - - +
118A GLU 4.1 0.4 + - - -
126A HIS 3.8 1.2 - - - +
127A ARG* 3.6 1.2 - - - -
128A VAL* 2.9 36.3 + - - +
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Residues in contact with VAL 117 (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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36A PHE* 3.1 10.1 - - - -
37A TYR* 2.7 63.1 + - + +
115A LEU* 4.2 18.8 - - + -
116A VAL* 1.3 76.3 - - - +
118A GLU* 1.3 60.1 + - - +
119A ILE* 3.7 17.8 - - + +
125A GLU* 3.9 29.2 - - + +
126A HIS 3.4 8.7 - - - +
127A ARG* 4.4 17.0 - - + -
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Residues in contact with GLU 118 (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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1A PHE* 3.7 42.2 - - + +
34A VAL* 4.3 11.2 - - + +
35A THR 3.8 3.4 - - - -
36A PHE* 3.9 24.5 - - + -
116A VAL 4.1 1.0 - - - -
117A VAL* 1.3 70.4 - - - +
119A ILE* 1.3 60.3 + - - +
120A ARG* 2.8 51.7 + - + -
124A SER 3.6 2.1 - - - +
125A GLU* 3.3 5.7 - - - -
126A HIS* 2.9 36.9 + - + +
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.8 2.6 - - - -
35A THR* 2.8 53.0 + - - +
36A PHE 4.2 1.1 - - - -
37A TYR* 3.8 25.1 - - + +
117A VAL* 3.7 27.4 - - + +
118A GLU* 1.3 71.7 - - - +
120A ARG* 1.3 59.9 + - - +
121A HIS* 3.5 25.4 - - - +
122A HIS* 5.4 1.3 - - - +
124A SER 3.8 2.7 - - - -
125A GLU* 4.4 17.7 - - + +
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Residues in contact with ARG 120 (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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1A PHE* 5.2 8.1 - - - +
33A ASP 4.7 6.8 - - - +
34A VAL* 3.8 27.6 - - + +
118A GLU* 2.8 36.5 + - + -
119A ILE* 1.3 74.1 - - - +
121A HIS* 1.3 68.4 + - - +
124A SER* 3.1 20.4 + - - +
126A HIS* 5.7 4.0 + - - +
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Residues in contact with HIS 121 (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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119A ILE* 3.4 20.4 - - - +
120A ARG* 1.3 81.4 - - - +
122A HIS* 1.3 87.0 + - + +
123A HIS* 3.3 11.7 + + - +
124A SER* 3.0 29.8 + - - +
125A GLU* 4.6 0.5 - - - +
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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