Contacts of the strand formed by residues 122 - 132 (chain A) in PDB entry 1XHU
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 PHE 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A SER 5.4 8.7 - - - -
3A PHE* 3.6 20.2 - + + -
118A VAL* 3.4 4.2 - - - +
119A LYS 3.0 35.6 + - - +
120A ASP 2.6 10.3 + - - +
121A GLN* 1.3 75.7 - - - +
123A TYR* 1.3 79.1 + - - +
124A GLU* 5.3 2.0 - - + -
162A ASP* 3.7 34.1 - - - -
163A LEU 3.2 23.3 - - - -
164A PHE 3.8 9.4 - - - -
165A ASP* 3.4 30.3 - - + -
223A ARG* 5.4 1.1 - - - -
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Residues in contact with TYR 123 (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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59A TYR* 3.4 29.9 + + - -
63A LEU* 5.9 0.3 - - - +
80A PHE 5.1 4.7 + - - -
85A LEU* 3.2 33.4 - - + +
89A LEU* 4.7 0.2 - - + -
116A LEU* 4.6 9.9 - - + -
117A LEU 3.6 2.5 - - - +
118A VAL* 3.2 33.0 - - + -
121A GLN* 4.1 25.7 + - - -
122A PHE* 1.3 84.9 - - - +
124A GLU* 1.3 61.6 + - - +
125A LEU* 4.0 15.0 - - + -
163A LEU* 2.9 34.2 + - + +
164A PHE* 3.1 7.5 - - + -
165A ASP 2.9 24.6 + - - -
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Residues in contact with GLU 124 (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 SER* 3.2 14.1 + - - -
3A PHE* 2.7 35.6 + - + -
4A ILE* 3.5 11.3 + - - +
115A ILE 3.4 2.9 - - - +
116A LEU* 3.5 2.1 - - - -
117A LEU* 2.9 60.7 + - + +
122A PHE* 5.4 1.6 - - + -
123A TYR* 1.3 75.5 - - - +
125A LEU* 1.3 65.2 + - - +
126A LEU* 3.4 10.0 + - - +
165A ASP* 3.6 7.4 - - + +
167A ASN* 2.3 42.1 + - + +
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Residues in contact with LEU 125 (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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85A LEU* 5.0 2.9 - - + -
88A LEU* 4.1 18.2 - - + -
89A LEU* 4.5 12.1 - - + -
112A THR* 4.0 22.0 - - + -
113A ALA* 3.7 19.3 - - + -
115A ILE 3.8 3.6 - - - -
116A LEU* 3.3 23.3 - - + -
123A TYR* 4.2 13.5 - - + -
124A GLU* 1.3 72.3 - - - +
126A LEU* 1.3 61.5 + - - +
127A ASP* 3.9 1.5 + - - +
164A PHE* 4.4 13.0 - - + -
165A ASP 2.8 13.4 + - - +
166A ILE* 3.7 30.7 - - + +
167A ASN 3.0 27.6 + - - +
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Residues in contact with LEU 126 (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 ILE* 3.2 32.5 - - + -
41A VAL* 5.1 3.4 - - + -
45A LEU* 4.0 14.1 - - + -
113A ALA* 4.8 0.4 - - - -
114A ASP* 3.1 7.3 + - - +
115A ILE* 2.8 59.6 + - + +
117A LEU* 4.8 8.5 - - + -
124A GLU* 3.4 6.7 + - + +
125A LEU* 1.3 73.1 - - - +
127A ASP* 1.3 64.3 + - - +
128A VAL* 4.8 7.0 - - + -
167A ASN* 3.5 21.3 - - + +
169A LEU* 4.0 26.0 - - + +
187A PHE* 4.4 12.6 - - + -
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Residues in contact with ASP 127 (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 THR 3.5 18.4 - - - +
113A ALA* 5.2 1.6 - - - -
114A ASP* 3.3 23.1 + - - +
125A LEU 5.1 1.8 - - - +
126A LEU* 1.3 76.0 - - - +
128A VAL* 1.3 67.1 + - - +
129A LYS* 2.9 36.3 + - - +
142A ILE 5.0 1.1 - - - -
166A ILE* 6.0 0.9 - - + -
167A ASN 3.1 5.8 + - - +
168A TYR* 3.4 27.8 - - + +
169A LEU 3.1 22.2 + - - -
7G C 5.8 3.2 - - - +
8H G 4.2 4.3 + - - -
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Residues in contact with VAL 128 (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 GLU* 3.7 40.4 - - + +
41A VAL* 5.1 7.9 - - + -
114A ASP* 3.0 23.6 + - + +
115A ILE* 5.3 3.8 - - + -
126A LEU* 4.8 10.1 - - + -
127A ASP* 1.3 79.1 - - - +
129A LYS* 1.3 68.5 + - - +
130A THR* 4.4 15.7 - - + -
169A LEU* 3.2 27.8 - - + +
171A VAL* 5.7 5.4 - - + -
8H G 5.6 2.2 - - - +
9H A 4.2 8.0 + - - +
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Residues in contact with LYS 129 (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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127A ASP* 2.9 22.7 + - - -
128A VAL* 1.3 78.6 - - - +
130A THR* 1.3 58.9 + - - +
131A ARG* 4.0 0.9 - - + -
140A PRO* 4.9 13.0 - - + -
141A ASN 3.1 18.1 + - - +
142A ILE* 2.6 46.4 + - + -
168A TYR* 3.6 19.7 - - + -
169A LEU 3.0 7.9 + - - +
170A GLU* 3.4 12.4 - - + +
171A VAL* 2.7 32.7 + - - +
212A VAL* 4.3 18.8 - - + -
7G C 6.2 1.6 - - - -
9H A 3.8 18.2 + - - +
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Residues in contact with THR 130 (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 ALA* 3.5 6.4 - - - +
34A GLY* 3.5 37.7 + - - +
37A PHE* 4.8 2.7 - - + -
38A GLU* 5.3 2.0 - - + +
128A VAL* 4.4 15.7 - - + -
129A LYS* 1.3 74.8 - - - +
131A ARG* 1.3 60.0 + - - +
171A VAL* 3.0 20.2 - - + +
173A TRP* 3.9 12.8 - - - -
9H A 3.0 32.7 + - - +
10H C 3.3 12.3 + - - -
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Residues in contact with ARG 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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129A LYS* 3.8 1.7 + - + -
130A THR* 1.3 70.6 - - - +
132A ASN* 1.3 61.9 + - - +
133A ILE* 2.9 28.3 + - + +
135A LYS 4.9 4.8 + - - +
136A SER* 4.5 16.0 + - - +
137A ALA 4.6 6.9 + - - +
170A GLU* 3.6 25.3 + - + +
171A VAL 2.8 8.5 + - - -
172A ASP* 3.3 16.1 - - - +
173A TRP* 2.7 37.3 + - - -
211A HIS* 2.9 55.5 + - + +
213A ARG* 4.0 21.3 - - - +
214A ASP* 5.1 1.6 + - - -
10H C 3.7 11.9 - - - +
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Residues in contact with ASN 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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28A LEU* 4.5 17.9 + - - +
131A ARG* 1.3 71.7 - - - +
133A ILE* 1.3 51.9 + - - +
134A SER* 2.8 37.0 + - - -
135A LYS* 3.5 30.5 - - + +
173A TRP* 3.3 45.2 - - + +
174A GLU* 4.6 0.2 - - - -
175A LEU 5.2 0.2 + - - -
10H C 2.9 29.6 + - - +
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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