Contacts of the strand formed by residues 140 - 144 (chain B) in PDB entry 3QUM
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 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A PHE* 4.5 0.8 - - - -
135A PHE* 4.6 4.5 - - - -
124B PRO* 4.1 0.3 - - - +
125B LEU* 3.1 40.5 + - - +
139B LEU* 1.3 76.6 - - - +
141B CYS* 1.3 64.1 + - - +
155B TRP* 3.6 7.3 - - - -
180B SER 3.6 11.4 - - - -
181B SER* 4.5 0.7 - - - -
211B ILE* 3.6 14.2 - - - +
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Residues in contact with CYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 5.1 7.0 - - - -
123B TYR 3.5 11.0 - - - -
124B PRO* 4.8 1.1 - - - -
125B LEU* 4.3 3.0 - - - +
140B GLY* 1.3 73.0 - - - +
142B LEU* 1.3 64.9 + - - +
143B VAL* 3.5 22.8 + - - +
153B LEU* 5.0 4.3 - - + +
155B TRP* 3.4 11.0 - - + -
178B LEU* 4.9 1.4 - - - +
179B SER* 3.6 1.1 - - - -
180B SER* 3.1 31.4 + - - +
196B CYS* 2.0 46.7 - - - -
198B VAL* 4.4 5.8 - - - -
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLN* 4.7 7.9 - - - +
131A SER* 4.4 21.8 - - - +
133A VAL* 4.7 18.2 - - + -
178A THR* 5.2 3.6 - - - +
122B VAL 3.7 0.2 - - - -
123B TYR* 2.8 74.9 + - + +
125B LEU* 4.3 19.3 - - + +
141B CYS* 1.3 71.6 - - - +
143B VAL* 1.3 62.2 + - - +
144B LYS* 3.9 30.1 - - + +
178B LEU 4.0 4.3 - - - +
179B SER* 4.1 11.7 - - - +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ALA* 5.3 3.1 - - + -
120B PRO 4.7 8.1 - - - +
121B PRO 4.3 2.0 - - - -
122B VAL* 4.0 12.6 - - + -
141B CYS* 3.5 13.3 + - - +
142B LEU* 1.3 76.3 - - - +
144B LYS* 1.3 61.1 + - - +
146B TYR* 4.1 26.7 - - + -
151B VAL* 4.9 1.1 - - + -
153B LEU* 4.6 4.7 - - + -
177B THR* 3.8 0.2 - - - -
178B LEU* 2.6 49.9 + - + +
198B VAL* 3.4 44.4 - - + -
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLN* 5.8 3.4 - - - +
131A SER* 5.1 9.1 + - - +
160A LEU* 5.1 6.7 - - - +
178A THR* 5.9 0.8 - - - +
180A THR* 4.9 15.4 - - - +
120B PRO* 2.9 36.0 - - - +
121B PRO* 3.7 8.7 + - - +
123B TYR* 5.5 7.4 - - + -
142B LEU* 3.9 28.5 - - + -
143B VAL* 1.3 77.6 - - - +
145B GLY* 1.3 58.5 + - - +
146B TYR* 3.7 2.5 - - - -
172B GLN* 5.7 2.4 + - - -
177B THR* 3.2 34.1 + - + +
178B LEU 5.1 0.2 - - - +
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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
------------------------------------------------------------
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