Contacts of the strand formed by residues 91 - 104 (chain B) in PDB entry 4LKC
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 ALA 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ARG* 3.9 10.8 - - + -
39B GLN 3.5 29.8 - - - +
40B ALA* 3.7 7.0 - - + +
41B THR 5.4 0.4 - - - +
88B GLY 5.9 0.2 - - - +
89B ASP 3.2 3.9 + - - +
90B THR* 1.3 77.2 - - - +
92B VAL* 1.3 62.1 + - - +
93B TYR* 3.3 21.9 - - + -
123B THR* 4.6 2.9 - - - -
124B VAL 2.9 30.5 + - - -
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Residues in contact with VAL 92 (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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37B VAL 4.1 0.5 - - - +
38B ARG* 3.3 4.2 - - - -
39B GLN* 3.0 37.2 + - + +
41B THR* 5.9 7.0 - - + -
91B ALA* 1.3 72.6 - - - +
93B TYR* 1.3 61.5 + - - +
94B TYR* 3.8 27.5 + - + +
120B GLN 4.5 2.2 - - - +
121B GLY* 3.8 25.4 - - - -
122B THR 3.4 9.4 - - - +
123B THR* 3.7 21.8 - - + +
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Residues in contact with TYR 93 (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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6B GLU* 4.0 2.9 - - - +
20B LEU* 3.6 29.4 - - + -
36B TRP* 4.4 6.3 - + + -
37B VAL 3.7 2.7 - - - -
38B ARG* 3.0 40.7 + - + -
48B VAL* 4.2 8.1 - - + -
67B PHE* 4.0 13.8 - + - -
80B LEU* 4.0 10.3 - - + -
82B MET* 4.0 17.0 - - - -
89B ASP* 2.5 35.1 + - - +
91B ALA* 3.3 23.8 - - + -
92B VAL* 1.3 74.1 - - - +
94B TYR* 1.3 61.9 + - - +
121B GLY* 3.3 2.4 - - - -
122B THR* 2.7 37.6 + - + +
124B VAL* 3.7 19.7 - - + +
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Residues in contact with TYR 94 (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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39A GLN* 3.7 16.2 + - - -
42A GLY 5.6 1.4 - - - -
43A LYS 3.9 9.0 + - - -
44A ALA* 3.7 23.1 - - + -
45A PRO* 4.6 3.1 - - + -
6B GLU* 3.3 3.8 - - - +
36B TRP* 3.2 13.5 - - - -
37B VAL 2.8 43.3 + - - +
39B GLN* 4.0 26.6 + - + -
45B LEU* 4.7 3.1 - - + -
92B VAL* 3.8 20.9 - - + +
93B TYR* 1.3 75.4 - - - +
95B CYS* 1.3 60.6 + - - +
96B VAL* 3.7 3.4 - - + +
118B TRP* 3.9 27.8 - + + -
119B GLY 3.3 18.2 - - - -
120B GLN 3.3 21.5 + - - -
121B GLY* 3.7 8.3 - - - -
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Residues in contact with CYS 95 (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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4B LEU* 3.4 9.2 - - + +
6B GLU* 2.7 21.1 + - + +
22B CYS* 2.0 53.6 - - + -
34B MET* 3.8 13.0 - - - -
35B HIS 3.8 3.8 - - - -
36B TRP* 4.0 7.4 - - + -
78B LEU* 3.7 16.4 - - - -
94B TYR* 1.3 70.5 - - - +
96B VAL* 1.3 60.9 + - - +
118B TRP* 3.5 1.9 - - - +
119B GLY 2.9 25.6 + - - -
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Residues in contact with VAL 96 (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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4B LEU* 4.1 0.2 - - - -
34B MET* 3.5 10.4 - - - +
35B HIS* 2.8 48.5 + - + +
37B VAL* 3.9 12.6 - - + -
94B TYR* 3.7 12.8 - - + +
95B CYS* 1.3 80.0 - - - +
97B ARG* 1.3 64.6 + - - +
115B MET* 3.5 39.7 - - + -
117B VAL 3.4 9.4 - - - +
118B TRP* 3.5 38.1 - - + -
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Residues in contact with ARG 97 (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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2B VAL* 4.0 10.3 - - - +
4B LEU* 3.8 6.1 - - + +
27B PHE* 3.3 58.1 - - + +
32B TYR* 3.6 38.6 + - + -
34B MET* 3.7 20.6 - - + -
35B HIS* 4.8 0.4 - - - -
96B VAL* 1.3 75.5 - - - +
98B GLU* 1.3 61.2 + - - +
115B MET* 3.4 8.7 - - - -
116B ASP* 2.8 58.8 + - - +
117B VAL* 2.8 34.1 + - + +
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Residues in contact with GLU 98 (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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92A PHE* 3.6 23.1 - - + -
97A ILE* 4.8 0.3 - - - +
32B TYR* 3.3 21.7 - - - +
33B ASP* 3.0 50.3 + - + +
35B HIS* 2.8 37.6 + - + +
96B VAL 4.1 0.4 + - - -
97B ARG* 1.3 71.9 - - - +
99B GLY* 1.3 70.6 + - - +
100B THR* 4.7 6.3 - - + +
113B TYR* 3.4 24.4 - - + -
114B GLY 3.5 8.1 - - - +
115B MET* 4.7 0.9 - - - +
116B ASP* 4.2 1.3 - - - -
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Residues in contact with GLY 99 (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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32B TYR* 4.8 6.5 - - - -
98B GLU* 1.3 79.8 - - - +
100B THR* 1.3 59.5 + - - -
101B TYR* 3.8 10.5 - - - -
113B TYR* 3.5 7.3 - - - -
114B GLY 2.7 34.9 + - - -
116B ASP* 3.7 24.4 + - - -
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Residues in contact with THR 100 (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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31B SER 6.1 1.3 - - - +
32B TYR* 5.4 9.0 - - + -
33B ASP* 6.2 3.8 - - + +
98B GLU* 4.1 9.2 + - - +
99B GLY* 1.3 74.2 - - - -
101B TYR* 1.3 69.3 + - - +
111B TYR* 4.9 12.5 - - + -
112B SER 3.6 4.3 - - - -
113B TYR* 3.7 25.8 - - + -
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Residues in contact with TYR 101 (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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47A LEU* 3.4 14.4 - - - +
50A TYR* 3.4 47.6 - + + +
56A GLU* 3.1 27.5 + - - -
99B GLY* 3.8 13.0 - - - -
100B THR* 1.3 78.1 - - - +
102B TYR* 1.3 61.0 + - - +
103B HIS 3.7 0.7 + - - -
111B TYR* 3.3 5.4 - - - -
112B SER* 2.7 56.7 + - - +
113B TYR 4.1 0.2 - - - -
114B GLY* 3.7 22.7 - - - -
116B ASP* 3.4 20.4 + - - +
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Residues in contact with TYR 102 (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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101B TYR* 1.3 73.1 - - - +
103B HIS* 1.3 60.0 + - - +
104B ASP* 3.4 43.7 + - + +
109B ASN* 3.1 28.3 + - + +
110B TYR* 3.3 27.4 - - - -
111B TYR* 3.5 46.4 - + + -
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Residues in contact with HIS 103 (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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51A ASP* 3.7 10.3 - - - +
54A SER* 5.1 7.4 - - - -
101B TYR 3.7 2.6 + - - +
102B TYR* 1.3 69.0 - - - +
104B ASP* 1.3 57.8 + - - +
105B SER* 4.0 22.6 - - - -
108B ASP 3.7 9.1 + - - -
109B ASN* 3.3 8.3 - - - +
110B TYR* 2.8 80.5 + + + +
112B SER* 5.6 2.9 + - - +
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Residues in contact with ASP 104 (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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102B TYR* 3.4 31.5 + - + +
103B HIS* 1.3 72.9 + - - +
105B SER* 1.3 59.8 + - - +
106B GLY 4.4 4.0 - - - +
109B ASN* 3.1 27.0 + - - +
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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