Contacts of the strand formed by residues 139 - 148 (chain B) in PDB entry 1EKV
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 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B LYS* 3.0 25.3 + - - +
80B ALA 3.4 14.1 - - - -
81B PHE* 3.7 18.8 - - - +
82B LYS 5.7 0.2 - - - +
132B VAL* 5.1 2.0 - - - -
133B PRO* 3.3 15.4 - - - +
137B GLY 5.3 0.4 - - - -
138B THR* 1.3 80.0 - - - +
140B LEU* 1.3 56.5 + - - +
169B PRO* 3.4 0.3 - - - +
170B VAL* 2.7 57.7 + - - +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B THR* 4.2 7.0 - - + -
79B LYS* 3.4 4.3 - - - -
80B ALA* 2.9 36.9 + - + +
125B ILE* 4.4 13.7 - - + -
128B ASP* 5.7 2.5 - - + +
131B TRP* 4.1 14.1 - - + +
132B VAL* 3.6 30.0 - - + +
133B PRO* 4.4 0.4 - - - +
139B SER* 1.3 77.9 - - - +
141B TYR* 1.3 65.1 + - - +
142B VAL* 3.7 2.7 + - + +
167B LEU* 3.8 35.7 - - + -
168B CYS* 3.4 30.5 - - - +
169B PRO* 3.4 9.6 - - + -
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Residues in contact with TYR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.9 16.4 - - + -
30B PHE* 3.5 33.8 - + + -
77B GLY* 3.0 20.8 - - - -
78B MET* 3.5 24.7 - - - -
79B LYS* 4.1 15.9 - - + -
139B SER 4.1 0.8 - - - -
140B LEU* 1.3 70.9 - - - +
142B VAL* 1.3 68.1 + - - +
143B ARG* 2.9 35.8 + - + -
166B ILE 3.9 0.2 - - - +
167B LEU* 3.3 9.2 - - - +
168B CYS* 2.7 42.9 + - - +
170B VAL* 3.7 16.7 - - + +
313B THR* 4.6 11.4 - - + -
314B ALA* 6.3 0.9 - - - -
371B TRS 4.3 16.1 + - - +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLY* 3.4 4.7 - - - -
78B MET* 2.6 68.9 + - + +
80B ALA* 4.4 2.5 - - + +
90B LEU* 4.3 11.7 - - + -
121B ILE* 4.0 10.1 - - + -
125B ILE* 4.0 22.2 - - + -
140B LEU* 4.0 9.6 - - + +
141B TYR* 1.3 77.3 - - - +
143B ARG* 1.3 60.6 + - - +
144B PRO* 3.2 8.7 - - + +
165B VAL* 4.0 12.6 - - + -
166B ILE 4.1 2.0 - - - -
167B LEU* 4.0 16.4 - - + -
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A HIS* 3.1 36.7 + - + -
70A TYR* 2.4 46.5 + - - -
153A LEU* 3.9 24.0 - - + +
30B PHE* 4.8 3.0 - - - -
75B PHE* 3.3 25.6 - - - -
76B GLU 3.1 12.6 - - - -
141B TYR* 2.9 37.9 + - + +
142B VAL* 1.3 73.2 - - - +
144B PRO* 1.3 63.9 - - - +
145B VAL* 3.9 2.6 - - + +
164B PHE 3.8 1.2 - - - +
165B VAL* 3.4 5.1 - - - -
166B ILE* 3.0 47.2 + - + +
168B CYS* 5.9 0.2 - - - -
371B TRS 5.4 1.4 + - - -
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Residues in contact with PRO 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PHE* 3.1 4.8 - - - +
76B GLU* 2.8 52.8 + - + +
78B MET* 3.7 27.1 - - + -
97B MET* 4.8 0.4 - - + -
100B MET* 4.0 25.6 - - + -
117B LEU* 5.3 1.3 - - + -
121B ILE* 4.2 7.9 - - + -
142B VAL* 3.2 14.1 - - + +
143B ARG* 1.3 84.7 - - - +
145B VAL* 1.3 62.4 + - - +
164B PHE 3.5 5.8 - - - +
165B VAL* 3.8 13.7 - - + -
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.5 11.0 - - + +
69A HIS* 3.5 32.1 - - + +
74B LEU 3.3 15.0 - - - +
75B PHE* 3.9 4.9 - - + +
100B MET* 4.3 4.0 - - - +
143B ARG* 3.9 11.9 - - + +
144B PRO* 1.3 82.4 - - - +
146B LEU* 1.3 63.7 + - - +
147B ILE* 3.7 22.4 - - + -
162B LEU 3.9 0.6 - - - +
163B LEU* 3.1 6.3 - - - +
164B PHE* 2.8 61.9 + - + +
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B TRP* 4.1 11.4 - - + -
73B GLN* 3.4 0.7 - - - -
74B LEU* 3.1 50.3 + - + +
100B MET* 4.0 7.0 - - + -
104B ALA* 4.1 15.0 - - + -
109B LEU* 3.9 24.5 - - + -
110B PRO* 3.9 21.8 - - + +
112B PHE* 4.5 12.6 - - + -
145B VAL* 1.3 75.6 - - - +
147B ILE* 1.3 64.2 + - - +
161B ALA* 4.4 6.5 - - + -
162B LEU 3.1 31.6 - - - +
163B LEU* 3.6 11.9 - - + -
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.1 21.5 - - + +
59B LEU* 5.5 0.7 - - + -
61B LEU* 4.5 15.3 - - + -
65B SER* 5.2 0.4 - - - +
67B SER* 3.5 24.7 - - - +
72B LEU 3.1 10.5 - - - +
73B GLN* 3.8 14.8 - - + -
109B LEU* 4.1 5.6 - - - -
145B VAL* 3.7 21.3 - - + -
146B LEU* 1.3 81.6 - - - +
148B GLY* 1.3 64.5 - - - +
149B ASN* 4.9 2.2 - - + -
161B ALA* 3.4 2.1 - - - +
162B LEU* 2.9 52.1 + - + +
164B PHE* 4.6 11.2 - - + -
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B SER* 3.6 6.1 - - - -
67B SER* 3.0 28.9 + - - -
72B LEU* 2.8 23.5 + - - -
109B LEU* 3.7 21.2 - - - +
147B ILE* 1.3 73.1 - - - +
149B ASN* 1.3 58.5 + - - +
158B PRO* 4.0 8.3 - - - -
160B ARG 4.0 3.8 - - - -
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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
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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