Contacts of the strand formed by residues 111 - 117 (chain A) in PDB entry 5H15
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 LEU 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A PHE* 3.9 17.3 - - + -
102A ASN 6.1 0.4 - - - -
105A SER* 5.2 7.6 - - - +
109A ASP 4.4 7.2 - - - +
110A PRO* 1.3 72.2 - - - +
112A VAL* 1.3 58.5 + - - +
124A TYR 4.1 0.2 - - - +
125A GLU* 3.5 2.1 - - - -
126A CYS* 2.8 46.0 + - + +
419A SER* 3.7 24.9 - - - +
420A ARG* 5.2 7.2 - - + +
421A ASP* 4.2 13.0 - - - +
423A SER* 4.1 9.0 - - - +
424A ILE* 3.7 26.0 - - + -
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Residues in contact with VAL 112 (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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101A PHE* 3.4 6.7 - - - -
102A ASN* 2.8 41.8 + - + +
105A SER* 5.3 2.0 + - - -
110A PRO* 3.3 13.5 + - + +
111A LEU* 1.3 78.5 - - - +
113A PHE* 1.3 62.7 + - - +
123A LEU* 4.3 5.8 - - + -
124A TYR 3.3 11.2 - - - +
125A GLU* 3.8 23.3 - - + +
135A LEU* 4.1 8.3 - - + -
152A TRP* 4.3 17.7 - - + -
68C VAL* 3.4 35.2 - - + -
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Residues in contact with PHE 113 (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 VAL* 3.7 18.2 - - + -
100A GLN 3.2 15.3 - - - +
101A PHE* 3.8 23.1 - + + -
102A ASN 4.5 0.2 - - - +
112A VAL* 1.3 78.1 - - - +
114A ALA* 1.4 58.9 + - - +
115A THR* 3.9 13.7 - - + -
122A THR 3.9 0.3 - - - +
123A LEU* 3.5 2.1 - - - -
124A TYR* 2.9 70.7 + + + -
126A CYS* 3.7 25.6 - - - -
132A ILE* 4.1 10.1 - - + -
152A TRP* 4.5 2.0 - - - -
426A ILE* 3.5 39.3 - - + -
434A ILE* 4.0 12.6 - - + -
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Residues in contact with ALA 114 (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 VAL* 3.2 7.6 - - - +
100A GLN 2.9 30.9 + - - +
113A PHE* 1.4 74.1 - - - +
115A THR* 1.3 61.5 + - - +
121A VAL* 4.8 2.9 - - + -
122A THR 3.2 6.1 - - - +
123A LEU* 3.8 21.1 - - + -
150A CYS* 4.3 11.8 - - - -
152A TRP* 3.9 14.1 - - + +
163A LEU* 3.8 18.2 - - + -
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Residues in contact with THR 115 (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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90A GLU* 2.7 24.5 + - - +
96A LEU* 4.3 10.1 - - + -
98A GLY 3.4 7.2 - - - -
99A VAL* 4.4 0.4 - - + -
113A PHE* 3.9 22.7 - - + -
114A ALA* 1.3 75.8 - - - +
116A VAL* 1.3 68.6 + - - +
120A ARG 3.9 0.5 - - - +
121A VAL* 3.4 1.9 - - - +
122A THR* 2.9 35.2 + - - -
124A TYR* 4.1 1.6 - - + -
428A VAL* 3.8 25.1 - - + -
434A ILE* 4.0 14.6 - - + -
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Residues in contact with VAL 116 (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 LEU* 3.4 8.0 - - - -
97A PHE* 2.8 30.5 + - - +
98A GLY* 2.9 34.6 + - - +
115A THR* 1.3 80.8 - - - +
117A GLY* 1.3 52.7 + - - +
120A ARG 3.5 2.2 - - - -
121A VAL* 3.9 15.3 - - + -
147A PHE* 3.9 13.2 - - + -
148A TYR 4.1 2.2 - - - -
149A THR 3.8 30.5 - - - +
150A CYS* 3.8 24.2 - - + +
165A VAL* 3.9 16.2 - - + -
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Residues in contact with GLY 117 (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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92A HIS* 4.6 3.8 + - - -
95A PRO 3.4 17.3 - - - -
96A LEU* 3.9 8.8 - - - +
97A PHE* 4.3 2.0 - - - -
116A VAL* 1.3 75.6 - - - +
118A SER* 1.3 72.4 + - - -
120A ARG* 2.9 27.2 + - - +
147A PHE* 3.8 11.0 + - - +
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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