Contacts of the strand formed by residues 131 - 139 (chain A) in PDB entry 5LF4
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A VAL* 3.4 8.2 - - - +
75A TYR* 4.6 5.4 - - + -
76A SER 3.4 9.4 - - - +
77A GLY 4.6 0.4 - - - -
78A MET 3.2 30.1 - - - +
81A ASP* 3.5 14.1 - - + -
82A TYR* 3.7 10.5 - - + +
85A LEU* 3.4 31.4 - - + -
117A MET* 3.4 19.6 - - + +
129A PHE* 3.2 4.1 + - + -
130A GLY* 1.3 83.2 - - - +
132A SER* 1.3 62.2 + - - +
133A LEU* 4.0 13.0 - - + -
150A PRO* 3.4 11.3 - - - +
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Residues in contact with SER 132 (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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25A LEU* 4.4 1.9 - - - +
28A VAL* 3.4 21.5 - - - +
75A TYR* 3.1 6.2 - - - +
76A SER 3.0 31.5 + - - -
131A VAL* 1.3 73.4 - - - +
133A LEU* 1.3 61.5 + - - +
147A GLN* 4.2 1.0 + - - -
148A SER 3.4 4.5 - - - -
149A ASP* 2.5 29.3 + - - -
150A PRO* 3.4 14.7 - - - +
162A MET* 3.4 21.0 - - - +
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 4.1 16.6 - - + -
74A VAL 3.4 3.6 - - - +
75A TYR* 4.0 2.7 - - + -
82A TYR* 3.6 36.1 - - + -
85A LEU* 4.2 11.0 - - + -
113A VAL* 3.7 30.3 - - + -
117A MET* 4.2 11.4 - - - -
131A VAL* 4.0 20.0 - - + -
132A SER* 1.3 74.3 - - - +
134A LEU* 1.3 59.5 + - - +
135A ILE* 4.1 17.9 - - + -
147A GLN* 3.1 10.4 - - - +
148A SER* 2.9 37.9 + - - +
162A MET* 4.3 0.7 - - - -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 4.3 0.7 - - - +
35A VAL* 3.7 16.4 - - - +
36A GLY* 3.6 29.8 - - - +
45A LEU* 4.0 10.8 - - + +
73A LEU* 3.2 5.4 - - - +
74A VAL* 2.8 49.8 + - + +
132A SER 4.2 0.4 + - - -
133A LEU* 1.3 72.3 - - - +
135A ILE* 1.3 60.5 + - - +
136A CYS 4.2 0.4 - - - -
145A LEU* 4.4 7.6 - - + -
146A PHE 3.2 12.3 - - - +
147A GLN* 3.9 14.6 - - + -
157A TRP* 4.8 0.4 - - + -
160A THR* 3.5 28.7 - - + -
162A MET* 3.8 24.9 - - + -
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Residues in contact with ILE 135 (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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71A ILE* 3.8 26.0 - - + -
72A GLY 3.4 2.9 - - - -
73A LEU* 3.2 25.4 - - + -
106A THR* 4.2 7.0 - - + -
109A LEU* 4.6 5.8 - - + -
110A VAL* 3.8 44.2 - - + +
113A VAL* 4.8 12.1 - - + -
133A LEU* 4.2 22.7 - - + +
134A LEU* 1.3 75.0 - - - +
136A CYS* 1.3 62.1 + - - +
144A TYR 3.9 0.9 - - - +
145A LEU* 3.5 4.1 - - - +
146A PHE* 2.7 44.9 + - + +
148A SER* 5.0 4.7 - - - -
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Residues in contact with CYS 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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43A VAL* 3.5 31.6 - - + -
45A LEU* 3.6 28.9 - - + +
71A ILE* 3.3 8.0 - - - +
72A GLY 2.8 36.2 + - - +
106A THR* 4.1 4.0 - - - -
134A LEU 4.2 0.8 + - - -
135A ILE* 1.3 74.7 - - - +
137A GLY* 1.3 57.8 + - - +
144A TYR 3.2 5.2 - - - +
145A LEU* 4.6 0.4 - - + +
211A ILE 5.0 0.4 - - - -
212A CYS* 3.6 23.1 - - + -
217A PHE* 3.6 18.8 - - - -
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Residues in contact with GLY 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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43A VAL* 4.3 1.9 - - - +
70A HIS 3.2 12.6 - - - -
71A ILE* 4.3 0.7 - - - -
106A THR* 3.2 21.2 - - - +
136A CYS* 1.3 78.1 - - - +
138A TRP* 1.3 59.3 + - - +
139A ASN 4.3 0.2 - - - -
143A PRO* 3.5 3.8 - - - +
144A TYR* 2.7 33.6 + - - +
212A CYS* 3.5 8.7 - - - -
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Residues in contact with TRP 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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40A ALA 4.7 1.1 - - - -
41A ASN* 3.4 39.7 - - + -
42A GLY* 3.8 1.3 - - - -
70A HIS* 3.3 27.5 + - + +
106A THR* 3.8 1.2 + - - -
137A GLY* 1.3 73.2 - - - -
139A ASN* 1.3 73.3 + - - +
141A GLY* 3.7 26.2 - - - +
142A ARG 3.4 14.8 - - - +
143A PRO* 3.5 37.0 - - + -
212A CYS* 4.2 5.8 - - - -
213A ASN* 3.6 28.0 - - - +
214A GLU* 3.6 50.5 - - + +
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Residues in contact with ASN 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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70A HIS* 3.9 9.1 - - + +
103A PRO 6.2 0.2 - - - +
105A PRO* 3.7 26.5 - - + +
106A THR* 2.7 39.3 + - - +
107A ALA 5.5 0.2 - - - +
138A TRP* 1.3 79.6 - - - +
140A GLU* 1.3 76.9 + - - +
141A GLY 3.1 4.0 - - - +
142A ARG* 3.1 17.2 + - - +
144A TYR* 3.6 24.9 + - - -
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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