Contacts of the strand formed by residues 134 - 142 (chain A) in PDB entry 3S8S
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 HIS 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.2 6.5 - - + +
102A ASN 4.1 3.4 + - - -
103A ASP* 3.5 46.7 - - + +
105A VAL 2.8 26.1 + - - -
106A ARG* 3.9 22.9 - - + +
125A ILE* 3.5 29.0 - - + +
127A LEU* 4.0 10.1 - - - +
132A ARG 4.0 0.6 + - - -
133A LYS* 1.3 76.2 - - - +
135A LEU* 1.3 62.5 + - - +
136A GLY* 2.9 38.2 + - - -
137A LEU 3.8 9.9 - - - -
190A PRO* 3.8 10.9 - - - +
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Residues in contact with LEU 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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126A LEU* 3.1 18.3 + - + +
127A LEU 3.6 15.7 - - - -
128A HIS* 3.6 32.1 - - + +
133A LYS 4.2 1.1 - - - +
134A HIS* 1.3 72.8 - - - +
136A GLY* 1.3 58.1 + - - +
137A LEU* 3.2 18.8 + - + +
180A TYR* 3.4 37.5 - - + -
183A ILE* 3.5 39.3 - - + +
184A VAL* 3.9 10.8 - - + -
190A PRO* 3.3 23.4 - - + +
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Residues in contact with GLY 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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99A ALA* 3.3 4.9 - - - -
100A ARG 3.1 11.9 + - - -
101A LEU* 2.9 47.7 + - - +
134A HIS* 2.9 20.4 + - - -
135A LEU* 1.3 78.8 - - - +
137A LEU* 1.3 58.4 + - - +
190A PRO* 4.1 6.4 - - - +
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Residues in contact with LEU 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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98A PHE 3.2 5.6 - - - +
99A ALA* 3.7 24.9 - - + -
100A ARG 4.9 0.4 - - - +
101A LEU* 4.3 0.7 - - - -
125A ILE* 3.5 3.3 - - - -
126A LEU* 3.1 41.7 + - + -
134A HIS* 3.8 5.6 + - - -
135A LEU* 3.2 24.2 - - + +
136A GLY* 1.3 80.6 - - - +
138A ALA* 1.3 62.9 + - - +
176A ARG* 3.9 12.8 - - + +
179A TYR* 3.7 24.2 - - + -
180A TYR* 3.5 39.5 - - + +
183A ILE* 4.2 7.6 - - + -
193A VAL* 5.1 1.1 - - + -
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Residues in contact with ALA 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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96A VAL 4.4 0.2 - - - -
97A THR* 3.4 5.9 - - - -
98A PHE* 2.9 36.1 + - + +
101A LEU* 3.6 13.7 - - + -
110A LEU* 3.4 30.3 - - + -
124A GLU 3.1 14.1 - - - +
125A ILE* 4.1 2.9 - - + +
126A LEU* 4.7 1.3 - - - +
137A LEU* 1.3 76.2 - - - +
139A ARG* 1.3 60.1 + - - +
140A VAL 4.3 0.2 - - - -
176A ARG* 3.7 10.9 - - - +
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Residues in contact with ARG 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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95A GLU* 2.9 44.4 + - + +
96A VAL 3.5 5.2 - - - -
122A GLU* 2.9 40.8 + - - +
123A VAL* 3.4 2.9 + - - -
124A GLU* 2.9 74.5 + - - +
126A LEU* 6.0 0.6 - - + +
138A ALA* 1.3 73.0 - - - +
140A VAL* 1.3 66.3 + - - +
141A LEU* 4.0 11.5 - - - +
176A ARG* 3.3 34.7 - - - +
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Residues in contact with VAL 140 (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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95A GLU* 3.4 3.9 - - - -
96A VAL 2.9 36.5 + - - +
98A PHE* 3.6 30.1 - - + -
110A LEU* 4.1 18.8 - - + -
114A CYS* 4.2 13.2 - - + -
120A VAL* 4.0 17.7 - - + -
122A GLU 3.4 9.2 - - - +
123A VAL* 4.2 8.5 - - + -
139A ARG* 1.3 80.2 - - - +
141A LEU* 1.3 62.1 + - - +
142A PHE* 3.6 30.5 - - + -
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Residues in contact with LEU 141 (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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94A LYS* 3.6 28.9 - - + +
95A GLU* 3.8 24.9 + - + +
120A VAL* 3.7 4.3 - - - +
121A GLU* 2.8 40.4 + - + -
122A GLU* 2.9 40.6 + - + +
139A ARG* 4.0 7.5 - - - +
140A VAL* 1.3 71.7 - - - +
142A PHE* 1.3 64.5 + - - +
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Residues in contact with PHE 142 (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 UNX 3.7 1.8 - - - -
94A LYS* 2.9 38.4 + - - +
96A VAL* 3.7 21.8 - - + -
114A CYS* 3.9 15.9 - - + -
118A GLY* 3.9 9.4 - - - -
119A GLU 3.4 15.3 - - - -
120A VAL* 3.8 17.3 - - + -
121A GLU* 3.9 5.0 - - - +
140A VAL* 3.6 30.1 - - + -
141A LEU* 1.3 79.8 - - - +
143A THR* 1.3 63.8 + - - +
144A SER 3.3 17.9 - - - +
147A GLY 3.8 9.2 - - - -
148A ALA* 3.6 13.9 - - + +
151A THR* 3.0 31.0 - - + -
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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