Contacts of the strand formed by residues 121 - 130 (chain B) in PDB entry 2QC1
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 PRO 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B ASN* 4.9 6.3 - - - +
54B VAL 3.2 10.5 - - - +
55B ARG* 4.1 13.5 - - + +
103B VAL* 3.5 2.1 - - - +
104B LYS* 3.1 57.0 + - + +
106B THR* 3.7 16.6 - - + -
119B THR 3.7 5.6 - - - +
120B PRO* 1.3 85.9 - - + +
122B ALA* 1.3 64.2 + - - +
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Residues in contact with ALA 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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53B ASN* 3.5 6.5 + - - +
54B VAL* 2.8 39.8 + - + +
56B LEU* 5.9 1.8 - - + +
102B ILE 3.1 15.0 - - - +
103B VAL* 4.0 11.0 - - + +
120B PRO 4.8 2.2 - - - +
121B PRO* 1.3 76.8 - - - +
123B ILE* 1.3 63.7 + - - +
124B PHE* 3.5 27.8 - - + -
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Residues in contact with ILE 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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41B ILE* 4.1 13.0 - - + -
51B THR* 3.4 31.9 - - + -
52B THR 3.3 6.3 - - - +
53B ASN* 4.8 8.3 - - + +
95B ASN* 4.5 0.5 - - - +
101B ALA* 2.9 20.1 - - - +
102B ILE* 2.9 45.8 + - + +
122B ALA* 1.3 75.6 - - - +
124B PHE* 1.3 61.7 + - - +
125B LYS* 5.0 10.1 - - + +
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Residues in contact with PHE 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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35B LEU* 3.9 15.5 - - + -
50B VAL 3.7 0.7 - - - +
51B THR* 3.2 4.3 - - - +
52B THR* 2.8 47.5 + - - +
54B VAL* 3.7 23.3 - - + -
56B LEU* 5.3 8.7 - - + -
92B LEU* 3.6 30.5 - - + -
95B ASN* 4.1 2.0 - - - -
101B ALA* 3.3 21.8 - - + -
103B VAL* 5.3 2.9 - - + -
122B ALA* 3.5 22.0 - - + -
123B ILE* 1.3 76.8 - - - +
125B LYS* 1.3 61.9 + - - +
126B SER* 4.1 2.5 - - - +
144B MET* 3.8 28.7 - - + -
146B LEU* 4.0 19.3 - - + -
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Residues in contact with LYS 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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49B ILE* 4.4 4.0 - - + -
50B VAL 3.4 5.2 - - - +
51B THR* 3.6 31.2 + - + +
92B LEU* 4.5 1.9 - - - +
94B ASN 3.5 1.9 - - - +
95B ASN* 3.0 24.9 + - - +
96B ALA* 2.9 35.2 + - + +
97B ASP* 3.6 42.0 + - + +
102B ILE* 6.0 6.5 - - - -
123B ILE* 5.0 8.3 - - + +
124B PHE* 1.3 76.2 - - - +
126B SER* 1.3 62.7 + - - +
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Residues in contact with SER 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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49B ILE* 3.3 7.8 - - - +
50B VAL* 2.9 48.9 + - - +
92B LEU* 5.5 1.2 - - - +
94B ASN 4.5 2.9 + - - -
96B ALA* 4.5 0.7 - - - -
124B PHE* 4.5 1.2 - - - +
125B LYS* 1.3 77.8 + - - +
127B TYR* 1.3 64.9 + - - +
142B CYS* 4.4 6.1 - - - -
143B SER 3.3 19.7 + - - -
144B MET* 3.3 35.5 - - - +
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ASN 3.9 13.5 - - - -
48B GLN* 3.4 26.1 + - - -
49B ILE* 4.6 7.0 - - + +
94B ASN* 4.7 8.3 + - - +
96B ALA* 4.5 10.1 - - + +
125B LYS 4.4 0.4 + - - -
126B SER* 1.3 74.6 - - - +
128B CYS* 1.3 77.7 + - - +
129B GLU* 2.6 36.9 + - + -
141B ASN 4.1 0.5 - - - +
142B CYS* 3.7 12.8 - - - -
143B SER* 3.7 10.5 + - - +
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Residues in contact with CYS 128 (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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48B GLN* 2.8 38.1 + - - +
50B VAL* 3.4 27.4 - - - -
126B SER 3.7 2.0 - - - -
127B TYR* 1.3 85.7 - - - +
129B GLU* 1.3 60.1 + - - +
140B GLN* 3.4 25.1 + - + +
141B ASN 3.3 4.7 - - - +
142B CYS* 2.0 47.8 - - - -
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Residues in contact with GLU 129 (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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48B GLN* 4.5 0.7 + - - -
127B TYR* 2.6 38.0 + - + -
128B CYS* 1.3 72.3 - - - +
130B ILE* 1.3 74.3 + - - +
131B ILE* 3.3 1.6 + - + +
140B GLN* 3.3 1.7 - - - -
141B ASN* 2.8 48.3 + - + +
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Residues in contact with ILE 130 (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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48B GLN* 3.3 34.4 - - + +
128B CYS 3.9 1.2 + - - -
129B GLU* 1.3 81.7 + - - +
131B ILE* 1.3 63.8 + - - +
132B VAL* 3.1 37.7 + - + +
137B PHE* 4.1 19.3 - - + +
139B GLU 3.7 9.4 - - - +
140B GLN* 4.3 11.4 - - + +
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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