Contacts of the helix formed by residues 59 - 74 (chain B) in PDB entry 1UMD
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 SER 59 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ALA* 3.2 18.0 - - - +
188A ASN* 6.2 0.2 - - - -
29B GLU* 3.6 3.0 + - - -
57B PRO* 2.9 12.5 + - - +
58B LEU* 1.3 75.8 - - - +
60B GLU* 1.3 60.3 + - - +
61B ALA* 3.5 4.0 + - - +
62B ALA* 3.0 28.9 + - - +
63B ILE* 2.9 30.7 + - - +
179C SER* 3.5 18.6 + - - -
180C GLU* 3.5 10.1 + - - -
181C GLY 4.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 2.7 20.7 - - - +
59B SER* 1.3 69.9 - - - +
61B ALA* 1.3 60.4 + - - +
63B ILE* 4.2 7.4 - - + -
64B VAL* 2.9 34.9 + - + +
81B ILE* 4.1 23.0 - - + +
82B GLN 5.6 1.2 + - - -
86B TYR* 2.9 25.1 - - - +
87B ILE 4.6 0.9 - - - +
89B PRO* 3.6 3.9 - - + +
90B GLY* 3.7 17.4 - - - +
180C GLU* 2.7 28.9 + - - +
2402C TPP 2.7 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO* 3.7 5.2 - - + +
182A ASP* 3.2 37.2 - - + +
185A ALA* 4.3 8.7 - - + -
59B SER* 3.2 7.3 + - - +
60B GLU* 1.3 77.8 - - - +
62B ALA* 1.3 58.4 + - - +
65B GLY* 2.9 26.7 + - - -
89B PRO* 3.8 12.4 + - - +
90B GLY* 3.6 12.0 - - - +
93B GLN* 3.4 10.7 - - - +
180C GLU* 5.2 0.4 + - - +
181C GLY* 6.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO* 4.6 8.7 - - - -
185A ALA* 3.7 21.2 - - - +
186A GLY* 4.8 0.9 - - - -
189A PHE* 4.0 22.7 - - + -
56B THR* 6.3 0.4 - - - -
57B PRO* 5.6 5.4 - - + +
59B SER* 3.0 27.8 + - - +
61B ALA* 1.3 77.8 - - - +
63B ILE* 1.3 57.2 + - + +
66B ALA* 2.9 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE* 5.3 0.9 - - - -
27B LEU* 4.0 18.2 - - + +
28B GLY* 4.1 5.8 - - - -
29B GLU* 3.6 25.8 - - - +
56B THR* 3.4 32.1 - - + +
57B PRO 4.5 0.4 - - - +
59B SER 2.9 19.9 + - - +
60B GLU* 3.8 9.2 - - - +
61B ALA 3.3 0.4 - - - -
62B ALA* 1.3 76.2 - - + +
64B VAL* 1.3 63.5 + - - +
67B ALA* 3.0 26.0 + - - +
79B ALA* 3.7 23.8 - - + -
80B GLU 3.9 22.4 - - - +
81B ILE* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU 2.9 23.4 + - - +
63B ILE* 1.3 73.0 - - + +
65B GLY* 1.3 59.5 + - - +
67B ALA* 3.3 6.8 + - - +
68B LEU* 3.0 26.0 + - - +
79B ALA* 5.2 2.0 - - + -
81B ILE* 3.8 23.6 - - + -
87B ILE* 4.2 15.9 - - + -
90B GLY* 4.3 4.3 - - - +
93B GLN* 3.8 6.1 - - + -
94B LEU* 3.7 34.1 - - + +
98B VAL* 3.8 17.9 - - + +
113B LEU* 4.8 0.7 - - + +
115B VAL* 4.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO* 3.8 10.1 - - - -
152A PRO* 3.2 9.9 - - - +
61B ALA 2.9 15.3 + - - -
64B VAL* 1.3 76.3 - - - +
66B ALA* 1.3 64.2 + - - +
68B LEU* 3.1 6.9 + - - +
69B GLY 2.9 18.4 + - - -
93B GLN* 3.1 28.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO 3.5 15.3 + - - +
154A ALA* 4.9 0.7 - - + -
155A GLY* 3.2 15.9 - - - +
158A ILE* 4.7 0.9 - - + -
189A PHE* 3.5 31.2 - - + -
27B LEU* 4.7 3.1 - - + -
62B ALA* 2.9 25.1 + - - +
63B ILE 4.1 1.3 - - - +
65B GLY* 1.3 69.0 - - - +
67B ALA* 1.3 61.3 + - - +
69B GLY 3.1 1.6 + - - -
70B MET* 2.8 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 4.4 3.3 - - + +
63B ILE 3.0 19.8 + - - +
64B VAL* 3.5 6.7 - - - +
66B ALA* 1.3 77.5 - - - +
68B LEU* 1.3 56.5 + - - +
70B MET* 3.2 7.9 + - - -
71B ALA* 2.9 27.2 + - - +
77B PRO* 3.3 27.2 - - + +
79B ALA* 4.0 21.3 - - + -
113B LEU* 3.9 11.7 - - + -
115B VAL* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 3.6 31.0 - - + -
152A PRO* 4.0 8.7 - - + -
64B VAL 3.0 14.2 + - - +
65B GLY* 3.3 11.4 - - - +
67B ALA* 1.3 77.6 - - - +
69B GLY* 1.3 58.2 + - - +
71B ALA* 3.2 1.4 + - - +
72B ALA* 2.9 28.2 + - - +
97B GLN* 3.9 15.0 - - + +
98B VAL* 3.7 33.2 - - + +
101B LEU* 3.9 11.2 - - + -
111B ALA* 3.5 32.5 - - + -
113B LEU* 3.5 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 5.4 2.2 - - - -
140A PHE* 5.7 0.2 - - - -
152A PRO* 3.3 30.5 - - - -
156A ALA* 3.6 13.0 - - - +
65B GLY 2.9 11.1 + - - -
66B ALA 3.1 2.4 + - - -
68B LEU* 1.3 78.7 - - - +
70B MET* 1.3 60.5 + - - +
72B ALA* 3.4 6.0 + - - +
73B HIS* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLY 3.3 16.5 - - - +
158A ILE* 3.4 43.3 - - + -
159A SER* 3.9 6.9 + - - -
189A PHE* 4.7 0.2 - - + -
25B VAL* 4.6 3.6 - - - -
27B LEU* 4.2 22.0 - - + -
54B MET* 4.0 16.4 - - + -
66B ALA* 2.8 30.4 + - + +
67B ALA* 3.5 13.7 - - - +
69B GLY* 1.3 71.4 - - - +
71B ALA* 1.3 56.5 + - - +
73B HIS* 3.3 0.9 + - - -
74B GLY 3.0 12.3 + - - -
75B LEU* 3.0 47.1 + - + +
77B PRO* 4.2 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA 2.9 16.8 + - - +
68B LEU 3.2 4.2 + - - +
70B MET* 1.3 76.2 - - - +
72B ALA* 1.3 65.5 + - - +
73B HIS 3.3 0.3 + - - -
74B GLY* 3.8 6.1 + - - -
75B LEU 3.3 12.4 - - - +
77B PRO* 3.9 4.5 - - + -
110B THR* 5.1 0.7 + - - -
111B ALA* 4.0 5.2 - - - -
112B PRO* 3.5 52.9 - - + +
113B LEU* 3.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP* 3.6 19.4 - - + -
92A PHE* 6.2 0.2 - - + -
140A PHE* 3.9 27.6 - - + -
68B LEU 2.9 17.0 + - - +
69B GLY* 3.8 5.4 - - - +
70B MET 3.3 0.2 - - - -
71B ALA* 1.3 77.0 - - - +
73B HIS* 1.3 60.6 + - - +
101B LEU* 4.2 5.2 - - + -
109B PHE* 4.9 7.0 - - + -
110B THR* 3.4 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP* 3.5 36.4 - + + -
156A ALA* 4.1 10.8 - - + -
159A SER* 2.8 30.9 + - - +
160A MET* 3.6 29.3 - - + +
163A LEU* 4.1 8.8 - - + +
165A THR* 4.0 11.9 - - + -
167A GLN* 2.8 28.2 + - - -
69B GLY 3.1 16.3 + - - +
71B ALA 3.2 0.4 - - - -
72B ALA* 1.3 79.7 - - - +
74B GLY* 1.3 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 4.2 16.3 - - - +
23B ARG* 3.2 30.1 + - - +
70B MET 3.0 2.8 + - - -
71B ALA 3.8 3.8 + - - -
72B ALA 3.7 1.0 - - - -
73B HIS* 1.3 81.4 + - - +
75B LEU* 1.3 67.3 + - - +
76B ARG* 4.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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