Contacts of the strand formed by residues 154 - 164 (chain A) in PDB entry 1XPM
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 GLY 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ALA* 4.1 10.9 + - - -
140A THR* 4.8 0.2 - - - -
141A ALA 2.8 28.8 + - - +
142A ARG* 5.5 0.3 - - - +
153A GLN* 1.3 78.3 - - - +
155A ALA* 1.3 62.5 + - - +
273A VAL 3.6 14.8 - - - -
274A GLY 4.2 0.2 - - - -
275A ASN 3.3 18.3 + - - -
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Residues in contact with ALA 155 (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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12A VAL* 3.8 5.9 - - - +
13A PRO* 3.3 24.8 - - + +
43A ALA* 3.7 14.6 - - + +
45A SER* 3.2 27.8 - - - +
54A MET* 4.4 5.4 - - - -
139A ASP 3.5 12.6 - - - +
140A THR* 4.2 9.4 - - + -
154A GLY* 1.3 75.5 - - - +
156A GLY* 1.3 58.8 + - - +
273A VAL* 4.0 0.2 - - - +
276A ILE* 3.5 14.1 - - - +
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Residues in contact with GLY 156 (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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11A TYR 3.2 13.9 - - - -
12A VAL* 4.3 2.5 - - - -
54A MET* 3.6 15.5 - - - +
138A THR* 3.6 0.7 - - - -
139A ASP 3.1 30.0 + - - +
155A ALA* 1.3 76.9 - - - +
157A ALA* 1.3 62.2 + - - +
276A ILE* 3.7 17.3 - - - +
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Residues in contact with ALA 157 (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 PHE* 3.2 5.2 - - - +
11A TYR 2.9 32.7 + - - +
54A MET 3.5 33.4 - - - +
55A GLY* 3.9 5.4 - - - -
58A ALA* 3.7 3.0 - - + +
136A ILE* 4.6 0.7 - - + -
137A ALA 3.0 13.7 - - - +
138A THR* 3.7 11.7 - - - +
156A GLY* 1.3 75.5 - - - +
158A VAL* 1.3 65.7 + - - +
276A ILE* 4.5 3.3 - - - +
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Residues in contact with VAL 158 (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 ILE* 4.2 11.0 - - + -
9A ASN 3.4 11.2 - - - +
10A PHE* 3.9 12.1 - - + -
58A ALA* 4.3 1.6 - - - -
135A VAL 3.9 0.9 - - - +
136A ILE* 3.4 3.4 - - - +
137A ALA* 2.8 38.6 + - + +
157A ALA* 1.3 79.7 - - - +
159A ALA* 1.3 63.8 + - - +
160A MET* 4.4 5.3 - - + +
276A ILE* 4.1 11.0 - - + -
279A GLY* 3.6 24.0 - - - +
282A TYR* 3.8 23.6 - - + -
283A LEU* 3.9 9.4 - - - +
286A ILE* 4.1 12.1 - - + -
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Residues in contact with ALA 159 (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 ILE* 3.3 4.9 - - - +
9A ASN 2.9 32.3 + - - +
58A ALA* 3.7 9.8 - - + +
59A ALA* 3.6 42.0 - - + +
62A ILE* 3.6 7.1 - - + +
134A LEU* 4.5 2.2 - - + -
135A VAL 3.4 6.5 - - - +
136A ILE* 4.2 7.2 - - + -
158A VAL* 1.3 74.8 - - - +
160A MET* 1.3 64.0 + - - +
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Residues in contact with MET 160 (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 ILE* 4.0 21.3 - - + -
7A LYS 3.4 6.7 - - - +
8A ILE* 3.7 21.1 - - + -
114A ALA* 4.6 4.0 - - + -
118A ILE* 3.7 25.4 - - + -
133A VAL 3.6 0.9 - - - +
134A LEU* 3.6 4.2 - - - +
135A VAL* 2.9 47.6 + - + +
137A ALA* 5.7 2.0 - - + -
158A VAL* 4.4 8.1 - - + +
159A ALA* 1.3 79.7 - - - +
161A VAL* 1.3 64.5 + - - +
162A ILE* 3.9 13.7 + - + +
282A TYR* 3.5 49.4 - - + -
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Residues in contact with VAL 161 (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 ILE* 3.7 2.6 - - - -
6A ASP* 2.8 36.0 + - + +
7A LYS* 3.0 21.7 + - + +
62A ILE* 4.2 19.7 - - + +
63A ILE* 3.6 30.7 - - + -
67A ASP* 5.1 3.4 - - - +
71A ILE* 5.5 2.9 - - + -
132A LYS* 3.8 32.5 - - + +
133A VAL 3.5 7.9 - - - +
134A LEU* 4.2 7.2 - - + -
160A MET* 1.3 74.6 - - - +
162A ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 162 (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 ILE* 4.1 11.7 - - + -
4A GLY* 3.2 14.4 - - - +
5A ILE* 3.9 27.1 - - + -
118A ILE* 4.0 30.5 - - + +
121A ALA* 4.1 27.4 - - + -
122A LYS* 4.2 6.7 - - + +
125A LEU* 3.4 14.1 - - + +
132A LYS* 3.3 4.3 - - - +
133A VAL* 2.8 39.8 + - + +
135A VAL* 4.4 6.1 - - + -
160A MET* 4.3 7.6 - - + +
161A VAL* 1.3 76.3 - - - +
163A ALA* 1.3 67.3 + - - +
171A LEU* 5.0 2.2 - - + -
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Residues in contact with ALA 163 (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 ILE* 3.4 6.7 - - - -
4A GLY 2.9 31.8 + - - +
6A ASP* 4.2 17.0 - - + +
125A LEU* 3.8 8.3 - - - -
131A GLU 4.6 1.1 - - - +
132A LYS* 3.7 33.0 - - + -
161A VAL* 4.0 1.0 + - + -
162A ILE* 1.3 76.9 - - - +
164A HIS* 1.3 70.3 + - - +
166A PRO* 3.5 4.2 - - - +
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Residues in contact with HIS 164 (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 ALA 3.4 7.2 + - - +
3A ILE* 3.6 24.6 - - + +
6A ASP* 5.0 1.2 - - - +
125A LEU* 2.6 38.3 + - + +
126A ALA 4.2 5.4 - - - -
128A ARG 3.2 19.5 + - - -
129A PRO* 3.5 28.3 - - + +
131A GLU 4.3 5.6 + - - -
163A ALA* 1.3 80.1 - - - +
165A ASN* 1.3 76.0 + - + +
295C GLN* 6.0 4.1 - - + +
296C ALA* 4.1 14.3 + - - +
320C GLU* 4.0 9.6 + - - -
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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