Contacts of the strand formed by residues 137 - 142 (chain A) in PDB entry 1X7H
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ASP* 3.4 14.6 - - - -
131A MET* 3.5 11.2 - - - -
136A THR* 1.3 85.5 + - - +
138A ARG* 1.3 83.2 + - - +
179A GLY 3.6 2.8 + - - -
180A ILE* 3.4 18.3 - - - -
181A THR 3.4 0.2 + - - -
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Residues in contact with ARG 138 (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 ASP 2.9 10.9 + - - +
86A VAL* 3.3 17.9 - - + +
87A LEU 2.9 25.6 + - - +
131A MET* 3.4 2.9 - - - +
136A THR* 5.5 1.2 + - - -
137A GLY* 1.3 81.0 + - - +
139A ILE* 1.3 64.2 + - - +
140A VAL* 4.2 9.6 - - + -
179A GLY 3.2 25.1 + - - -
181A THR* 3.2 31.3 + - - +
239A LEU* 3.0 26.2 + - + +
240A ILE* 3.5 20.1 + - + -
241A GLY 3.2 25.5 + - - -
242A PRO* 4.2 5.3 - - - +
244A ALA 4.3 0.4 - - - -
245A ALA* 4.0 22.0 - - - +
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Residues in contact with ILE 139 (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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87A LEU* 3.5 28.5 - - + +
122A THR* 4.2 8.7 - - + -
125A VAL* 5.9 0.2 - - + -
126A LEU* 3.7 31.2 - - + -
131A MET* 3.8 17.0 - - - -
138A ARG* 1.3 77.1 - - - +
140A VAL* 1.3 66.1 + - - +
141A ASN* 3.9 18.2 - - - +
171A LEU* 4.1 18.2 - - + -
175A LEU* 4.6 0.2 - - + -
180A ILE* 4.2 5.6 - - + -
181A THR* 2.9 15.0 + - - +
182A VAL* 3.3 20.7 - - + -
183A ASN* 3.0 26.0 + - - +
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Residues in contact with VAL 140 (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 VAL* 5.3 3.8 - - + -
87A LEU 2.8 13.8 + - - +
88A VAL* 3.3 14.6 - - + +
89A ASN 2.9 23.7 + - - -
138A ARG* 4.7 12.3 - - + -
139A ILE* 1.3 82.3 - - - +
141A ASN* 1.3 66.6 + - - +
142A ILE* 4.6 4.9 - - + -
183A ASN* 3.4 7.9 - - + +
185A VAL* 3.9 27.4 - - + -
236A VAL* 4.3 26.5 - - + +
239A LEU* 4.6 21.8 - - + -
240A ILE* 5.4 1.3 - - + +
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Residues in contact with ASN 141 (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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89A ASN* 2.9 29.1 - - + +
118A VAL* 3.2 18.4 - - + +
122A THR* 4.2 0.5 - - - +
139A ILE* 3.9 7.7 - - - +
140A VAL* 1.3 74.2 - - - +
142A ILE* 1.3 63.2 - - - +
143A ALA 3.3 0.7 + - - -
164A VAL* 3.7 19.9 + - + -
167A PHE* 4.3 7.3 - - - -
168A THR* 2.8 34.4 + - - +
182A VAL* 4.1 13.7 - - - +
183A ASN 2.9 6.8 + - - +
184A ALA* 3.0 7.0 - - + +
185A VAL 2.9 24.1 + - - -
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Residues in contact with ILE 142 (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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18A ILE* 4.7 3.6 - - + -
22A ILE* 3.9 22.7 - - + -
88A VAL* 4.3 9.6 - - + -
89A ASN 2.9 25.5 + - - +
90A ASN* 3.6 24.5 - - + +
91A ALA* 5.2 1.9 + - - +
140A VAL* 4.6 3.1 - - + -
141A ASN* 1.3 73.6 - - - +
143A ALA* 1.3 58.9 + - - +
161A LYS* 3.3 17.5 + - - +
164A VAL* 4.7 5.3 - - - +
185A VAL* 3.6 17.7 - - + -
187A PRO* 3.8 22.4 - - + -
232A VAL* 4.7 4.0 - - + -
236A VAL* 4.5 6.7 - - + -
301A NDP 3.3 30.2 + - - +
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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