Contacts of the strand formed by residues 129 - 136 (chain L) 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 129 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124L GLN* 2.5 38.0 + - - +
125L LEU* 4.8 1.3 + - - -
127L SER* 3.8 0.7 + - - -
128L GLY* 1.3 77.2 - - - +
130L ALA* 1.3 60.2 + - - -
181L LEU 4.5 0.4 - - - -
182L THR* 3.5 7.0 - - - -
183L LYS* 3.2 23.2 - - - +
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Residues in contact with ALA 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L PRO* 3.4 19.5 - - + +
124L GLN* 3.0 14.8 - - + +
125L LEU* 3.3 32.5 - - + -
129L GLY* 1.3 75.9 - - - +
131L SER* 1.3 60.0 + - - +
132L VAL* 5.5 1.2 - - - +
179L LEU 4.4 0.9 - - - +
180L THR* 4.6 1.1 + - - -
181L LEU* 2.7 36.7 + - - +
182L THR 4.2 1.2 - - - -
186L TYR* 4.4 11.1 - - + +
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Residues in contact with SER 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H LEU* 6.0 2.3 - - - +
141H LEU* 3.6 21.0 - - - +
143H LYS* 4.4 4.0 - - - +
118L PHE 5.0 0.3 - - - +
120L PRO* 4.0 17.4 - - - +
124L GLN* 2.8 26.5 + - - +
130L ALA* 1.3 74.0 - - - +
132L VAL* 1.3 61.9 + - - +
133L VAL* 4.1 5.9 + - - +
178L THR* 4.1 9.2 - - - +
179L LEU 3.3 4.3 - - - -
180L THR* 3.2 36.8 + - - -
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Residues in contact with VAL 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L ILE* 4.5 16.6 - - + -
118L PHE 3.0 24.5 - - - +
120L PRO* 4.7 9.4 - - + -
130L ALA 5.5 0.9 - - - +
131L SER* 1.3 75.7 - - - +
133L VAL* 1.3 60.6 + - - +
148L TRP* 4.1 13.5 - - + -
177L SER 3.9 0.9 - - - +
178L THR* 3.4 4.7 + - - -
179L LEU* 2.8 52.8 + - + +
186L TYR* 6.0 2.5 - - + -
192L TYR* 5.2 15.5 - - + -
209L PHE* 4.1 24.0 - - + -
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Residues in contact with VAL 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 3.4 35.7 - - + -
141H LEU* 4.4 19.7 - - + -
178H SER* 5.6 3.4 - - - +
116L SER 3.9 0.2 - - - +
117L ILE* 3.4 9.3 - - - +
118L PHE* 3.3 33.6 + - + -
131L SER 4.5 3.4 - - - +
132L VAL* 1.3 80.3 - - - +
134L CYS* 1.3 59.5 + - - +
135L PHE* 3.6 26.0 - - + -
148L TRP* 4.7 1.1 - - - -
176L SER* 6.5 0.7 - - - -
177L SER 3.8 4.3 - - - +
178L THR* 3.5 16.8 - - - +
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Residues in contact with CYS 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L VAL* 4.2 14.8 - - - -
116L SER 3.4 6.7 - - - -
117L ILE* 3.6 13.2 - - - -
133L VAL* 1.3 74.8 - - - +
135L PHE* 1.3 66.4 + - - +
136L LEU* 4.1 11.0 - - + +
146L VAL* 5.7 0.4 - - + -
148L TRP* 4.2 1.3 - - + -
175L MET 4.0 0.2 - - - +
176L SER* 3.6 6.9 - - - -
177L SER* 3.1 38.5 + - - +
194L CYS* 2.0 53.4 - - - -
207L LYS 4.9 0.2 - - - -
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Residues in contact with PHE 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H LEU* 5.0 6.1 - - + -
137H THR* 5.2 3.4 - - - +
139H GLY 5.5 2.2 - - - -
140H CYS 5.5 0.2 - - - -
166H PHE* 3.7 30.7 - + - -
178H SER* 4.1 14.8 - - - -
179H SER 4.4 6.3 - - - -
180H SER* 2.6 43.3 - - - -
114L THR 3.2 6.1 - - - +
115L VAL* 3.2 6.0 - - - -
116L SER* 2.7 45.8 + - - +
118L PHE* 4.4 11.4 - + - -
133L VAL* 3.6 33.0 - - + -
134L CYS* 1.3 80.5 - - - +
136L LEU* 1.3 62.7 + - - +
137L ASN* 3.4 14.0 - - - +
175L MET 4.1 2.9 - - - -
176L SER* 5.3 1.6 - - - -
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Residues in contact with LEU 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L PRO* 4.6 10.1 - - + -
114L THR 4.8 0.2 - - - -
115L VAL* 4.3 21.8 - - + +
134L CYS* 4.1 15.5 - - + +
135L PHE* 1.3 80.5 - - - +
137L ASN* 1.3 74.5 + - - +
139L PHE* 4.2 13.7 - - + -
144L ILE* 3.2 40.2 - - + -
146L VAL* 4.3 10.3 - - + -
174L SER* 3.1 11.8 + - - -
175L MET* 3.2 41.8 + - + +
176L SER* 5.5 0.2 - - - -
177L SER* 5.8 1.1 - - - +
196L ALA* 5.7 2.9 - - + -
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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