Contacts of the strand formed by residues 106 - 114 (chain A) in PDB entry 3PHM
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ALA* 4.3 1.6 - - + -
102A SER 3.2 20.9 + - - +
103A MET 4.5 0.2 - - - +
105A THR* 1.3 81.7 - - + +
107A HIS* 1.3 62.9 + - - +
108A HIS 3.6 9.0 - - - +
109A MET* 3.5 33.0 - - + -
141A TRP* 3.6 23.2 - - + -
143A ARG* 2.9 18.7 + - - +
171A VAL* 3.7 14.4 - - + -
172A HIS 3.6 4.3 - - - +
173A TYR* 4.0 2.7 - - + +
187A SER* 3.4 31.6 - - - +
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Residues in contact with HIS 107 (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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105A THR 3.2 2.2 + - - -
106A VAL* 1.3 73.4 - - - +
108A HIS* 1.3 61.1 + - + +
141A TRP* 4.4 1.1 - - - -
142A ALA* 4.0 0.5 - - - +
143A ARG* 3.0 44.7 + - + +
172A HIS* 2.8 34.5 + + + +
174A GLY* 4.1 13.9 - - - +
271A PRO* 6.0 7.0 - - + -
357A CU 2.2 27.1 - - - -
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Residues in contact with HIS 108 (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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79A TYR* 3.5 23.6 - + - -
106A VAL* 3.6 2.4 - - - +
107A HIS* 1.3 82.1 - - + +
109A MET* 1.3 72.3 + - - +
110A LEU* 3.4 29.0 - - + +
141A TRP* 3.1 15.3 - - - +
142A ALA* 4.4 6.5 - - + -
170A GLN* 2.9 23.2 + - - +
172A HIS* 2.9 43.1 + - + +
240A ARG* 5.4 4.2 + - - -
272A GLN 5.9 2.2 - - - +
357A CU 2.0 31.5 - - - -
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Residues in contact with MET 109 (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 PRO* 3.9 9.6 - - + -
101A ALA* 3.4 28.3 - - + -
106A VAL* 3.5 14.8 - - + -
108A HIS* 1.3 80.1 - - - +
110A LEU* 1.3 70.4 + - - +
139A TYR* 4.5 1.3 - - - -
140A ALA* 3.2 0.3 - - - -
141A TRP* 2.7 59.4 + - + +
169A LEU* 4.6 6.5 - - + -
170A GLN 3.2 8.3 - - - +
171A VAL* 4.0 16.2 - - + -
187A SER* 4.5 1.8 - - - -
188A GLY* 3.3 44.9 - - - +
189A VAL* 4.2 7.9 - - + -
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Residues in contact with LEU 110 (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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108A HIS* 3.4 22.0 - - + +
109A MET* 1.3 84.2 - - - +
111A LEU* 1.3 59.3 + - - +
112A PHE* 3.8 32.8 - - + -
137A ILE* 4.4 5.2 - - + -
139A TYR* 3.3 5.6 - - - +
140A ALA* 3.6 23.8 - - + -
168A VAL 3.9 0.7 - - - +
169A LEU* 3.6 5.4 - - - +
170A GLN* 2.8 54.0 + - + +
189A VAL* 6.0 0.2 - - - -
240A ARG* 4.0 28.7 - - - +
272A GLN 5.2 0.7 - - - +
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Residues in contact with LEU 111 (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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66A ILE* 3.8 21.5 - - + -
97A PHE* 4.0 19.5 - - + -
110A LEU* 1.3 75.4 - - - +
112A PHE* 1.3 64.1 + - - +
137A ILE* 3.7 3.8 - - - +
138A LEU* 2.9 27.1 + - + -
139A TYR* 2.8 27.1 + - + +
167A PHE* 4.0 16.8 - - + -
168A VAL 3.4 21.5 - - - +
169A LEU* 4.0 17.7 - - + -
189A VAL* 4.3 6.7 - - + -
191A VAL* 3.6 30.5 - - + -
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Residues in contact with PHE 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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110A LEU* 3.8 37.7 - - + -
111A LEU* 1.3 73.9 - - - +
113A GLY* 1.3 62.1 + - - +
130A THR* 3.7 26.5 - - + -
131A CYS* 4.8 0.7 - - - -
135A ALA* 3.8 30.3 - - + -
136A ASN 3.3 6.5 - - - +
137A ILE* 3.7 35.4 - - + -
138A LEU* 4.1 5.6 - - - +
167A PHE* 3.1 9.5 - - - +
168A VAL* 2.8 47.5 + - + +
170A GLN* 4.2 17.5 - - + -
318A TYR* 6.1 1.8 - + - -
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Residues in contact with GLY 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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112A PHE* 1.3 75.6 - - - +
114A CYS* 1.3 61.2 + - - +
135A ALA* 3.9 0.2 - - - -
136A ASN* 2.8 38.3 + - - +
138A LEU* 3.9 9.4 - - - +
164A SER* 3.1 20.5 + - - -
166A TYR 3.4 7.9 - - - -
167A PHE* 4.5 1.3 - - - -
702A GOL 3.8 6.5 - - - -
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Residues in contact with CYS 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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113A GLY* 1.3 73.9 - - - +
115A ASN* 1.3 66.3 + - - +
116A MET 4.0 5.4 - - - -
117A PRO* 4.0 6.3 - - - -
131A CYS* 2.1 48.2 - - - -
133A ASP* 3.5 11.9 - - - +
134A LYS 3.5 12.3 - - - +
136A ASN* 5.2 1.1 - - - +
164A SER* 3.2 5.8 + - - +
165A LYS 3.3 2.9 + - - -
166A TYR* 2.9 35.1 + - - +
168A VAL* 3.5 16.6 - - - -
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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