Contacts of the strand formed by residues 130 - 138 (chain A) in PDB entry 1HFP
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A SER* 5.7 4.5 - - - -
4A LEU* 4.2 17.8 + - - +
129A GLY* 1.3 70.0 - - - -
131A LEU* 1.3 67.4 + - - +
132A LYS* 4.4 15.0 + - + +
183A GLU* 2.7 43.5 + - + +
184A LYS 2.3 31.5 + - - -
185A ASN* 3.3 29.1 - - + +
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Residues in contact with LEU 131 (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 LEU* 3.5 47.1 - - + +
5A ASN 4.1 0.4 - - - +
6A CYS* 4.1 17.7 - - - -
124A ALA* 3.7 23.3 - - + +
125A MET* 4.1 4.9 - - - +
127A HIS* 5.8 0.9 - - + +
129A GLY 3.6 1.7 + - - +
130A HIS* 1.3 77.5 + - - +
132A LYS* 1.3 67.1 + - - +
133A LEU* 3.6 17.5 - - + -
156A TYR* 3.3 26.6 - - + +
182A TYR 4.1 0.2 - - - +
183A GLU* 3.6 2.1 - - - -
184A LYS* 3.0 45.9 + - - +
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Residues in contact with LYS 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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3A SER* 4.5 12.6 + - - -
4A LEU 3.5 4.0 + - - -
5A ASN* 3.3 25.7 - - - +
6A CYS 3.0 24.4 + - - +
130A HIS* 4.4 16.1 + - - +
131A LEU* 1.3 81.5 - - - +
133A LEU* 1.3 63.0 + - - +
134A PHE* 3.8 15.5 - - + -
159A LEU* 5.0 1.1 - - + -
162A TYR* 3.8 28.4 + - + +
181A VAL* 4.2 17.9 - - + -
182A TYR 3.1 10.8 - - - +
183A GLU* 4.0 23.3 + - + +
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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
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6A CYS* 3.6 21.1 - - + -
8A VAL* 6.4 0.2 - - + -
125A MET* 4.2 20.6 - - + -
131A LEU* 3.6 31.2 - - + -
132A LYS* 1.3 74.3 - - - +
134A PHE* 1.3 61.0 + - - +
135A VAL* 3.8 8.8 + - + -
148A PHE* 5.1 5.4 - - + -
151A ILE* 4.2 29.6 - - + -
156A TYR* 3.9 32.5 - - + -
180A GLU 3.7 0.7 - - - +
181A VAL* 3.4 5.2 - - - +
182A TYR* 2.8 43.5 + - + +
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Residues in contact with PHE 134 (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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5A ASN* 3.8 7.4 - - - -
6A CYS 2.9 14.0 + - - +
7A ILE* 3.4 17.6 - - + +
8A VAL* 3.2 26.5 + - - +
33A TYR* 3.9 24.9 - + + +
37A MET* 4.6 9.2 - - - -
113A TRP* 3.6 35.7 - + - -
132A LYS* 3.8 30.3 - - + -
133A LEU* 1.3 72.4 - - - +
135A VAL* 1.3 59.0 + - - +
136A THR* 4.2 0.7 - - - -
162A TYR* 4.0 34.5 - + - -
165A VAL* 4.6 4.5 - - + -
180A GLU 3.4 5.6 - - - +
181A VAL* 4.0 21.3 - - + -
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Residues in contact with VAL 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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8A VAL* 3.6 17.5 - - + -
10A VAL* 3.9 22.0 - - + -
33A TYR* 6.3 0.4 - - - -
133A LEU* 4.1 12.8 - - + +
134A PHE* 1.3 75.8 - - - +
136A THR* 1.3 61.2 - - - +
137A ARG* 3.7 29.6 + - + +
148A PHE* 5.5 2.0 - - + -
151A ILE* 4.5 10.8 - - + -
179A PHE* 3.6 1.2 - - - -
180A GLU* 2.8 43.4 + - - +
182A TYR* 3.7 31.6 - - + -
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Residues in contact with THR 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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8A VAL 2.9 10.4 + - - -
9A ALA* 3.4 3.7 - - - -
10A VAL* 3.0 27.5 + - - +
30A GLU* 2.7 44.6 + - + +
33A TYR* 4.0 4.5 - - - -
134A PHE 4.2 0.9 + - - -
135A VAL* 1.3 72.4 - - - +
137A ARG* 1.3 58.0 + - - +
138A ILE* 3.6 12.0 + - + -
177A TYR* 3.7 22.7 - - + -
178A LYS 3.4 4.7 - - - +
179A PHE* 3.4 20.5 - - + -
188A MOT 3.5 6.4 + - - -
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Residues in contact with ARG 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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10A VAL* 3.9 13.7 - - - +
11A SER 5.7 1.5 + - - -
14A MET* 4.0 29.1 - - - +
135A VAL* 3.8 14.6 - - + +
136A THR* 1.3 69.3 - - - +
138A ILE* 1.3 59.7 + - - +
139A MET* 3.4 6.2 + - + +
151A ILE* 3.8 15.7 - - - +
177A TYR* 3.0 6.6 - - - -
178A LYS* 2.7 54.5 + - - +
180A GLU* 2.8 35.8 + - + +
182A TYR* 2.9 28.7 + - - -
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Residues in contact with ILE 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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9A ALA* 4.4 7.0 - - + -
10A VAL 2.8 18.2 + - - +
11A SER* 3.5 4.3 - - - -
12A GLN* 3.2 21.0 + - - -
24A TRP* 4.0 29.6 - - + +
27A LEU* 3.5 31.2 - - + -
30A GLU* 4.5 2.5 - - + -
136A THR* 3.6 16.8 + - + -
137A ARG* 1.3 68.4 - - - +
139A MET* 1.3 58.8 + - - +
140A GLN 3.1 8.9 + - - +
142A PHE* 3.5 35.7 - - + -
175A ILE* 3.7 16.8 - - + -
177A TYR* 3.9 16.8 - - + -
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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