Contacts of the strand formed by residues 158 - 169 (chain A) in PDB entry 2LHS
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 ASN 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLU* 3.7 34.3 - - - +
34A GLY 2.9 20.6 + - - +
35A LEU* 4.4 8.5 - - - +
36A LYS* 3.5 4.7 - - - -
153A ILE* 3.0 31.4 + - + +
156A THR* 2.7 32.2 + - - +
157A ALA* 1.3 81.2 + - - +
159A ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 159 (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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33A GLU* 5.3 1.3 - - - -
34A GLY* 3.0 25.5 + - - -
35A LEU 3.2 5.9 + - - +
36A LYS* 3.7 17.1 - - + +
38A PHE* 4.5 9.9 - - + -
150A VAL* 4.0 7.6 - - + -
151A TRP 3.4 9.4 - - - +
152A ASP* 3.6 30.1 - - - +
153A ILE* 5.4 0.4 - - - -
158A ASN* 1.3 77.6 - - - +
160A PHE* 1.3 61.4 + - - +
161A TYR* 5.6 0.4 - - + -
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Residues in contact with PHE 160 (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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11A ALA* 6.0 0.2 - - + -
32A VAL* 3.5 28.3 - - + +
33A GLU* 3.2 30.2 + - - +
34A GLY 3.7 7.6 - - - +
38A PHE* 5.7 0.4 - - - -
49A ALA 3.2 22.9 - - - -
50A SER 3.9 0.2 - - - -
51A ALA* 3.6 18.6 - - + -
56A PHE* 3.5 37.7 - + + -
59A LEU* 4.6 5.6 - - + -
81A TRP* 5.5 0.2 - - - -
149A ALA 3.5 1.9 - - - +
150A VAL* 3.3 22.8 - - - +
151A TRP* 3.6 11.4 + - - +
159A ALA* 1.3 75.2 - - - +
161A TYR* 1.3 78.5 + - - +
162A GLN* 3.6 23.2 + - + +
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Residues in contact with TYR 161 (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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38A PHE* 3.5 65.7 - + - +
48A ILE* 4.7 1.1 + - + +
49A ALA* 3.3 20.3 + - - +
93A ARG* 4.9 7.4 + - + -
95A PHE* 3.3 41.6 - + - -
148A LEU* 4.0 20.6 - - + -
149A ALA 3.4 4.7 - - - -
150A VAL* 3.4 38.6 - - + +
159A ALA* 5.6 0.9 - - + -
160A PHE* 1.3 91.3 - - - +
162A GLN* 1.3 61.9 + - - +
163A ALA 3.5 3.1 + - - -
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Residues in contact with GLN 162 (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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2A GLY 3.4 20.4 + - - -
3A TYR* 3.4 10.2 - - - +
4A VAL* 3.1 30.7 + - + +
9A SER* 3.5 22.7 + - - +
11A ALA* 4.9 3.9 - - + +
32A VAL* 3.8 14.6 - - + +
81A TRP* 3.5 23.3 - - - -
147A ILE 3.9 0.7 - - - +
148A LEU* 3.7 0.2 - - - -
149A ALA* 2.7 37.3 + - + +
151A TRP* 5.3 4.4 - - - +
160A PHE* 3.7 26.3 + - + +
161A TYR* 1.3 69.4 - - - +
163A ALA* 1.3 61.9 - - - +
164A ILE* 3.9 2.3 + - - +
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Residues in contact with ALA 163 (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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9A SER* 2.8 20.9 + - - -
10A ARG* 2.8 27.3 + - - +
49A ALA* 4.3 6.1 - - + -
59A LEU* 3.7 24.9 - - + +
107A LEU* 5.3 0.2 - - + -
146A VAL* 3.9 19.7 - - + -
147A ILE 3.5 5.8 - - - -
148A LEU* 3.9 17.5 - - + +
161A TYR 3.5 3.8 + - - -
162A GLN* 1.3 73.5 - - - +
164A ILE* 1.3 52.6 + - - +
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Residues in contact with ILE 164 (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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4A VAL* 6.4 0.7 - - + -
7A PRO* 3.7 38.1 - - + +
8A ALA 3.2 31.2 - - - +
9A SER* 4.0 6.1 - - - +
10A ARG 4.2 2.2 - - - +
13A GLN* 4.0 2.9 - - - +
70A LEU* 4.1 17.9 - - + -
72A LEU* 4.5 1.1 - - + -
146A VAL* 3.3 4.5 - - - +
147A ILE* 2.9 55.6 + - + +
149A ALA* 6.2 2.5 - - + -
162A GLN 5.1 1.8 - - - +
163A ALA* 1.3 73.7 - - - +
165A ASP* 1.3 71.9 + - - +
166A VAL* 3.7 20.3 + - + +
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Residues in contact with ASP 165 (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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10A ARG* 4.0 11.5 - - + +
13A GLN* 4.6 0.8 - - - +
62A GLN* 3.7 14.4 - - - +
63A THR 4.4 0.3 - - - +
67A TRP* 3.4 39.1 - - + -
68A ASN 3.4 17.7 - - - +
69A LYS* 2.8 42.8 + - + -
70A LEU 3.4 4.9 + - - -
101A TRP* 4.7 1.2 - - - -
145A HIS 3.2 17.8 - - - +
146A VAL* 3.8 10.7 + - + +
164A ILE* 1.3 82.4 - - - +
166A VAL* 1.3 58.2 + - - +
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Residues in contact with VAL 166 (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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7A PRO* 5.9 0.2 - - + -
69A LYS* 3.6 9.9 - - - +
70A LEU* 3.5 15.3 - - + +
72A LEU* 4.2 13.5 - - + -
144A SER* 3.3 3.3 - - - -
145A HIS* 2.9 68.5 + - + +
147A ILE* 3.9 22.0 - - + -
164A ILE* 3.7 28.0 - - + +
165A ASP* 1.3 79.2 + - - +
167A ASN* 1.3 60.3 + - - +
168A LEU* 3.9 11.4 - - + -
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Residues in contact with ASN 167 (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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69A LYS* 3.8 17.8 - - + +
70A LEU 2.8 15.8 + - - +
71A ASN* 3.0 37.8 + - - +
72A LEU 3.5 1.9 + - - +
143A GLY* 3.7 5.3 - - - -
144A SER* 3.9 21.5 + - - +
166A VAL* 1.3 71.7 - - - +
168A LEU* 1.3 63.3 + - - +
169A SER* 5.3 0.3 + - - -
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Residues in contact with LEU 168 (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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72A LEU* 3.4 35.0 - - + +
73A LYS 4.1 5.6 - - - +
74A THR* 3.5 23.1 - - + +
137A ILE* 3.7 25.4 - - + -
141A ARG 3.3 18.6 - - - +
142A SER* 4.1 0.2 - - - -
143A GLY* 2.7 41.4 + - - +
145A HIS* 3.7 12.3 - - + -
147A ILE* 4.7 4.9 - - + -
166A VAL* 3.8 19.7 - - + -
167A ASN* 1.3 79.6 + - - +
169A SER* 1.3 65.4 + - - +
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Residues in contact with SER 169 (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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72A LEU 3.1 12.8 + - - -
73A LYS* 3.3 14.3 - - - +
74A THR* 2.9 30.7 + - - +
142A SER* 4.2 6.1 - - - -
167A ASN 5.3 0.2 - - - -
168A LEU* 1.3 76.2 - - - +
170A LYS* 1.3 63.9 + - - +
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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