Contacts of the strand formed by residues 119 - 126 (chain B) in PDB entry 3V4V
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 GLN 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ARG* 5.8 1.2 - - - +
82B GLY* 3.7 15.4 - - - +
83B GLN 3.4 41.6 + - - +
84B GLN* 3.5 21.2 - - - +
111B VAL* 4.3 10.1 - - + -
112B THR 4.1 2.7 - - - +
113B LEU* 3.5 24.2 - - + +
114B ARG 5.9 0.4 - - - +
117B GLU* 3.2 12.7 + - - +
118B PRO* 1.3 70.3 - - - +
120B GLN* 1.3 59.5 + - - +
121B LEU* 3.9 3.1 + - + +
422B VAL 3.7 1.4 - - - +
423B SER* 3.7 1.0 - - - -
424B LEU* 3.0 32.5 + - + +
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B GLN* 4.0 8.8 + - - +
118B PRO 3.5 6.1 + - - +
119B GLN* 1.3 74.7 + - - +
121B LEU* 1.3 59.4 + - - +
122B GLN 4.1 0.3 + - - -
390B GLU* 4.6 3.1 - - - +
399B ARG* 3.4 26.3 + - - +
421B TRP* 3.7 40.2 - - + +
422B VAL 3.3 11.9 - - - +
423B SER* 3.9 16.9 + - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B GLN* 3.2 24.0 + - - +
109B VAL* 4.2 18.8 - - + -
111B VAL* 3.7 29.6 - - + -
119B GLN* 3.9 3.0 - - + +
120B GLN* 1.3 75.3 - - - +
122B GLN* 1.3 60.2 + - - +
123B VAL* 3.6 25.6 - - + -
420B PHE 4.0 0.2 - - - +
421B TRP* 3.7 4.6 - - - -
422B VAL* 3.2 50.4 + - + +
424B LEU* 4.7 11.9 - - + -
438B LEU* 4.8 6.5 - - + -
447B LEU* 4.9 2.9 - - + -
449B VAL* 4.9 10.3 - - + -
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B GLN* 4.7 1.8 - - - +
106B PRO* 3.7 17.5 - - - +
120B GLN 4.1 0.6 + - - -
121B LEU* 1.3 76.0 - - - +
123B VAL* 1.3 69.3 + - - +
124B ARG* 4.3 26.3 + - - +
392B GLN* 5.5 0.2 + - - -
419B THR* 3.3 35.4 + - + +
420B PHE 3.7 3.8 - - - +
421B TRP* 3.8 33.7 - - + -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU* 3.6 33.7 - - + -
105B ALA 3.9 3.6 - - - +
106B PRO* 5.1 0.4 - - + -
121B LEU* 3.6 17.9 - - + -
122B GLN* 1.3 80.4 - - - +
124B ARG* 1.3 63.7 + - - +
125B PHE* 6.1 0.7 - - + -
376B LEU* 4.3 28.5 - - + -
419B THR* 3.5 1.9 - - - +
420B PHE* 2.7 46.8 + - + +
422B VAL* 4.5 4.7 - - + -
438B LEU* 4.7 0.4 - - + -
447B LEU* 3.6 26.5 - - + -
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ASP* 3.5 28.5 + - - -
91B PRO* 6.0 2.6 - - - +
92B LEU* 3.8 25.0 - - + +
103B GLN 3.8 0.3 - - - +
104B LEU* 3.7 4.9 - - - +
105B ALA* 3.2 49.3 + - - +
106B PRO* 4.3 8.5 - - - +
122B GLN* 4.3 29.1 + - - +
123B VAL* 1.3 77.0 - - - +
125B PHE* 1.3 60.9 + - - +
417B THR* 4.6 4.7 - - + -
418B VAL 3.4 10.8 - - - +
419B THR* 4.2 11.2 - - + +
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Residues in contact with PHE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 4.5 0.2 - - - -
103B GLN* 3.2 52.7 - - + -
104B LEU* 4.4 11.9 - - + -
123B VAL* 4.4 0.6 + - + -
124B ARG* 1.3 75.5 - - - +
126B LEU* 1.3 59.5 + - - +
127B ARG* 3.8 23.3 - - + -
374B VAL* 3.6 40.4 - - + -
412B VAL* 5.7 0.9 - - + -
416B GLN 4.0 0.7 - - - +
417B THR* 3.3 7.6 - - - +
418B VAL* 3.0 45.8 + - + +
420B PHE* 4.6 7.2 - - + -
440B ALA* 4.0 25.6 - - + -
443B PHE* 3.7 20.6 - + - -
445B GLU* 4.5 3.8 - - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 3.9 37.2 - - + +
93B SER 3.9 26.4 - - - +
94B GLN* 4.1 13.2 - - + +
103B GLN* 2.8 31.7 + - - +
125B PHE* 1.3 77.3 - - - +
127B ARG* 1.3 64.8 + - - +
128B ALA* 3.2 5.6 + - + +
415B ASN* 3.7 24.0 - - - +
416B GLN 3.5 11.0 - - - +
417B THR* 3.3 21.8 - - - +
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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