Contacts of the strand formed by residues 128 - 137 (chain A) in PDB entry 1WMA
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 ILE 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.2 35.7 - - + +
84A ASP 4.2 7.6 - - - +
86A LEU* 4.2 8.1 - - + -
124A LEU 3.8 7.0 - - - +
125A LEU* 3.1 24.0 + - + +
126A PRO 4.6 1.0 - - - +
127A LEU* 1.3 78.0 - - - +
129A LYS* 1.3 70.5 + - - +
132A GLY* 4.0 15.9 - - - -
134A VAL* 3.9 24.9 - - + -
211A LEU* 6.2 0.9 - - + -
215A ARG* 2.9 31.3 + - - +
220A ILE* 3.9 22.9 - - + -
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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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3A GLY* 5.5 0.8 + - - -
4A ILE 4.6 10.5 + - - -
5A HIS* 6.1 0.4 - - - +
6A VAL* 6.1 0.6 - - - +
80A TYR* 2.8 25.1 + - - +
81A GLY* 3.6 24.4 - - - +
82A GLY* 3.9 7.4 - - - -
83A LEU 3.0 12.3 + - - +
84A ASP* 3.6 29.2 + - - +
127A LEU 3.9 6.1 - - - +
128A ILE* 1.3 79.5 - - - +
130A PRO* 1.3 78.8 - - + +
132A GLY* 2.9 17.3 + - - -
215A ARG* 4.1 1.8 - - - -
220A ILE* 3.7 2.3 - - - +
306A SO4 3.1 36.8 + - - +
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Residues in contact with PRO 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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84A ASP* 4.7 4.2 - - - +
129A LYS* 1.3 95.7 - - + +
131A GLN* 1.3 70.4 + - + +
132A GLY 3.2 0.3 + - - -
215A ARG* 4.1 6.9 - - - +
218A ASP* 3.2 41.5 - - + +
220A ILE* 4.4 0.2 - - + -
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Residues in contact with GLN 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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84A ASP* 5.9 0.8 - - - +
130A PRO* 1.3 75.9 - - + +
132A GLY* 1.3 63.8 + - - +
133A ARG* 3.3 25.5 + - - +
218A ASP 2.8 14.1 + - - +
219A LYS* 2.7 47.5 - - + +
258A PRO* 3.0 47.8 + - + +
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Residues in contact with GLY 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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84A ASP* 3.0 21.3 - - - -
85A VAL* 5.4 0.7 - - - -
128A ILE* 4.0 5.8 - - - -
129A LYS 2.9 18.4 + - - -
130A PRO 3.1 1.0 + - - -
131A GLN* 1.3 78.5 - - - +
133A ARG* 1.3 75.6 + - - -
220A ILE* 3.4 10.4 - - - +
221A LEU 3.2 11.8 + - - -
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Residues in contact with ARG 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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84A ASP 3.0 6.4 + - - +
85A VAL* 3.2 11.3 - - + +
86A LEU 3.0 23.2 + - - +
128A ILE* 4.7 0.4 - - - +
131A GLN* 3.3 27.0 + - - +
132A GLY* 1.3 96.2 + - - -
134A VAL* 1.3 66.6 + - - +
135A VAL* 4.3 0.7 - - - -
219A LYS 2.9 21.4 + - - -
221A LEU* 3.2 40.1 - - + +
253A LEU 3.6 21.8 - - - +
254A ALA* 3.5 27.6 - - - +
255A LEU 5.1 0.2 - - - -
256A LEU* 2.9 22.1 + - + +
257A PRO 2.9 29.9 + - - -
258A PRO* 3.9 2.4 + - - +
260A ALA* 4.6 1.4 + - - +
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Residues in contact with VAL 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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86A LEU* 3.3 12.1 - - + +
88A ASN* 4.4 7.4 - - - +
121A CYS* 5.4 0.9 - - - -
125A LEU* 3.7 29.6 - - + -
128A ILE* 3.9 21.8 - - + -
133A ARG* 1.3 79.0 - - - +
135A VAL* 1.3 67.3 + - - +
136A ASN* 3.9 18.2 - - - +
211A LEU* 5.7 0.2 - - + -
220A ILE* 5.0 5.2 - - + -
221A LEU 3.0 6.9 + - - +
222A LEU* 3.2 32.1 - - + -
223A ASN* 3.1 26.0 + - - +
253A LEU 5.2 0.7 - - - +
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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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86A LEU 2.9 10.4 + - - +
87A VAL* 3.4 13.5 - - + +
88A ASN 2.8 26.3 + - - -
133A ARG 5.1 0.4 - - - -
134A VAL* 1.3 81.0 - - - +
136A ASN* 1.3 66.7 + - - +
137A VAL* 3.9 1.4 + - + -
223A ASN 3.5 3.1 - - - +
225A CYS* 3.9 26.0 - - - -
250A PRO* 3.8 22.0 - - + +
253A LEU* 3.6 17.5 - - + +
254A ALA* 3.5 39.3 - - + +
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Residues in contact with ASN 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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88A ASN* 2.8 35.0 + - + +
117A THR* 4.9 6.0 - - - +
121A CYS* 4.5 6.1 - - - -
134A VAL* 3.9 7.2 - - - +
135A VAL* 1.3 73.5 - - - +
137A VAL* 1.3 60.8 + - - +
138A SER 3.2 1.9 + - - -
200A VAL* 4.0 16.0 + - + +
203A LEU* 5.2 3.8 - - - +
204A SER* 2.9 39.1 + - - +
207A HIS* 5.3 2.8 + - - -
222A LEU* 4.0 14.3 - - - +
223A ASN 2.9 9.7 + - - +
224A ALA* 3.2 1.7 - - - +
225A CYS* 2.9 28.7 + - - -
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Residues in contact with VAL 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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16A ILE* 5.5 1.1 - - + -
20A ILE* 4.7 0.9 - - + -
87A VAL* 4.3 12.8 - - + -
88A ASN 2.9 25.3 + - - +
89A ASN* 3.7 26.0 - - + +
90A ALA 5.5 0.7 - - - +
135A VAL* 4.8 0.7 - - + -
136A ASN* 1.3 69.7 - - - +
138A SER* 1.3 61.0 + - - +
197A LYS* 3.0 20.3 + - - -
200A VAL* 4.1 7.2 - - - +
225A CYS* 3.9 15.3 - - - +
227A PRO* 4.0 20.4 - - + -
250A PRO* 4.6 10.1 - - + -
309A NDP 3.4 32.8 + - - +
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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