Contacts of the strand formed by residues 121 - 129 (chain A) in PDB entry 2O9C
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 LEU 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A THR* 3.8 30.7 - - + +
44A ALA 3.6 13.9 - - - +
52A LEU* 3.8 17.3 - - + -
53A GLN* 4.2 0.4 - - - +
117A ARG* 3.3 6.0 - - - +
118A VAL* 2.9 38.3 + - + +
119A GLY 3.3 0.4 - - - -
120A GLU* 1.3 78.5 - - - +
122A LEU* 1.3 64.3 + - - +
123A ILE* 4.1 8.8 + - + +
239A ASN* 3.7 21.5 - - - +
241A GLN* 3.7 18.1 + - - +
246A THR* 3.7 29.8 - - + -
247A PRO* 5.4 3.8 - - + -
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Residues in contact with LEU 122 (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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43A THR* 3.1 7.1 - - - -
44A ALA* 2.8 39.2 + - + +
45A ASP 4.2 2.9 - - - +
46A GLY* 3.8 24.7 - - - +
74A LEU* 4.9 3.4 - - + -
82A TRP* 3.7 20.6 - - + -
85A LEU* 3.6 25.6 - - + -
86A GLN* 5.7 2.0 - - + -
89A LEU* 4.1 19.5 - - + +
115A VAL* 4.3 2.5 - - + -
116A HIS 3.5 5.4 - - - +
117A ARG* 4.0 35.4 - - + +
120A GLU 4.2 0.2 + - - -
121A LEU* 1.3 72.7 - - - +
123A ILE* 1.3 62.0 + - - +
124A LEU* 3.7 14.9 - - + +
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Residues in contact with ILE 123 (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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41A LEU* 3.8 32.8 - - + -
42A LEU 3.7 3.1 - - - -
43A THR* 4.2 4.5 - - + -
114A THR 3.6 1.4 - - - +
115A VAL* 3.2 5.2 - - - -
116A HIS* 2.8 66.5 + - + +
118A VAL* 4.2 11.9 - - + -
121A LEU* 4.2 16.8 - - + +
122A LEU* 1.3 77.6 - - - +
124A LEU* 1.3 61.5 + - - +
125A GLU* 4.1 3.0 + - + +
246A THR* 4.2 11.7 - - + -
247A PRO* 3.2 27.6 - - + +
248A LEU* 4.4 5.8 - - + -
251A ALA* 4.5 2.7 - - + -
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Residues in contact with LEU 124 (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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40A ALA 3.9 0.2 - - - +
41A LEU* 3.2 6.3 - - - +
42A LEU* 2.8 48.5 + - + +
44A ALA* 4.3 6.1 - - + -
74A LEU* 3.9 43.3 - - + -
78A LEU* 4.1 8.1 - - + -
85A LEU* 4.4 6.3 - - + -
113A LEU* 4.0 17.0 - - + -
114A THR 3.5 3.8 - - - -
115A VAL* 3.9 14.6 - - + -
122A LEU* 3.7 24.5 - - + +
123A ILE* 1.3 75.6 - - - +
125A GLU* 1.3 62.3 + - - +
126A PHE* 3.8 22.0 - - + -
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Residues in contact with GLU 125 (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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40A ALA 3.5 4.3 - - - -
41A LEU* 4.0 18.6 - - + -
98A GLN* 5.6 0.5 + - - -
112A SER 3.3 2.0 - - - +
113A LEU* 3.3 6.1 - - - +
114A THR* 2.8 60.9 + - - +
116A HIS* 4.5 5.2 + - - -
123A ILE* 4.8 3.8 - - + +
124A LEU* 1.3 75.7 - - - +
126A PHE* 1.3 61.6 + - - +
127A GLU* 5.6 2.5 - - + +
250A GLY 4.2 4.2 - - - +
251A ALA* 3.5 23.2 - - + +
252A VAL* 3.1 8.6 + - - +
253A LEU* 2.9 43.2 + - + +
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Residues in contact with PHE 126 (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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39A GLY* 3.2 5.2 - - - -
40A ALA* 2.8 53.3 + - + +
42A LEU* 3.8 31.0 - - + -
61A PHE* 4.7 2.3 - - + -
62A LEU* 3.7 33.9 - - + -
74A LEU* 6.0 0.2 - - + -
78A LEU* 4.7 10.8 - - + -
103A LEU* 3.8 26.7 - - + -
111A LEU* 4.2 16.2 - - + -
112A SER 3.3 5.8 - - - -
113A LEU* 3.8 23.6 - - + -
124A LEU* 3.8 26.7 - - + -
125A GLU* 1.3 76.1 - - - +
127A GLU* 1.3 62.3 + - - +
128A PRO* 4.5 0.3 - - - +
253A LEU* 4.2 1.4 - - - +
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Residues in contact with GLU 127 (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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38A HIS* 4.0 17.4 + - + +
39A GLY* 4.3 3.1 - - - -
111A LEU* 3.8 5.5 - - - +
112A SER* 2.8 39.9 + - - +
125A GLU* 5.6 2.8 - - + +
126A PHE* 1.3 76.6 - - - +
128A PRO* 1.3 76.0 - - + +
252A VAL* 5.3 2.3 - - - +
253A LEU* 4.2 18.7 - - + +
296A VAL* 3.6 17.5 - - + +
299A PRO* 3.7 20.6 - - + +
302A ARG* 2.9 44.7 + - - +
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Residues in contact with PRO 128 (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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38A HIS 3.4 19.5 - - - +
61A PHE* 3.5 26.7 - - + -
105A TRP* 3.6 28.3 - - + -
110A HIS 3.4 8.3 - - - +
111A LEU* 3.8 3.5 - - + -
127A GLU* 1.3 96.2 - - + +
129A THR* 1.3 60.0 + - - +
296A VAL* 5.6 3.3 - - - +
299A PRO* 5.2 1.4 - - - +
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Residues in contact with THR 129 (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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102A THR* 5.0 6.3 - - + +
105A TRP* 5.2 0.4 - - - -
108A ALA 4.7 0.6 - - - +
109A GLY* 3.3 2.0 - - - -
110A HIS* 2.7 61.7 + - + +
111A LEU 4.7 0.4 - - - -
112A SER* 4.4 20.0 - - - +
127A GLU 4.4 2.9 - - - -
128A PRO* 1.3 76.2 - - - +
130A GLU* 1.3 71.9 + - - +
133A ASP* 4.1 13.5 + - - +
298A PRO* 4.7 1.0 - - - +
299A PRO* 3.9 17.2 - - - +
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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